Compositions and methods for the detection of hiv-1/hiv-2 infection

ABSTRACT

This invention relates to compositions and methods or the detection of immunodeficiency virus infection, especially immunodeficiency virus-1 (HIV-1) infection. The invention particularly concerns compositions and methods that may be used in HIV vaccine recipients whose sera may contain vaccine-generated anti-HIV-1 antibodies.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. Patent Applications Ser. Nos.60/676,931 (filed on May 3, 2005) and 60/607,579 (filed on Sep. 8,2004), which applications are each herein incorporated by reference intheir entirety.

FIELD OF THE INVENTION

This invention relates to compositions and methods for the detection ofimmunodeficiency virus infection, especially human immunodeficiencyvirus-1 (HIV-1) infection. The invention particularly concernscompositions and methods that may be used in HIV vaccine recipientswhose sera may contain vaccine-generated anti-HIV-1 antibodies.

BACKGROUND OF THE INVENTION

The human immunodeficiency virus (HIV) is a pathogenic retrovirus(Varmus, H. (1988) “RETROVIRUSES,” Science 240:1427-1439; Cowley S.(2001) “THE BIOLOGY OF HIV INFECTION” Lepr Rev. 72(2):212-20). HIV-1 isthe causative agent of acquired immune deficiency syndrome (AIDS) andrelated disorders (Gallo, R. C. et al. (1983) “Isolation of human T-cellleukemia virus in acquired immune deficiency syndrome (AIDS),” Science220(4599):865-7; Barre-Sinoussi, F. et al. “ISOLATION OF AT-LYMPHOTROPIC RETROVIRUS FROM A PATIENT AT RISK FOR ACQUIRED IMMUNEDEFICIENCY SYNDROME (AIDS),” (1983) Science 220:868-870; Gallo, R. etal. (1984) “FREQUENT DETECTION AND ISOLATION OF CYTOPATHIC RETROVIRUSES(HTLV-III) FROM PATIENTS WITH AIDS AND AT RISK FOR AIDS,” Science224:500-503; Teich, N. et al. (1984) “RNA TUMOR VIRUSES,” Weiss, R. etal. (eds.) Cold Spring Harbor Press (NY) pp. 949-956).

Since 1987, more than 25,000 individuals have received immunizationswith human immunodeficiency virus (HIV) preventive vaccines. Currently,most of the HIV vaccine candidates are complex products containingmultiple viral genes or proteins. Prime-boost strategies are under wayto optimize cellular and humoral immune responses. Consequently, vaccinerecipients' sera are often reactive in licensed HIV serodetectionassays, generating patterns indistinguishable from HIV-infectedindividuals (Ackers, M. L. et al. (2003) “HUMAN IMMUNODEFICIENCY VIRUS(HIV) SEROPOSITIVITY AMONG UNINFECTED HIV VACCINE RECIPIENTS,” J InfectDis 187:879-986; Pitisuttithum, P. et al. (2003) “SAFETY ANDIMMUNOGENICITY OF COMBINATIONS OF RECOMBINANT SUBTYPE E AND B HUMANIMMUNODEFICIENCY VIRUS TYPE 1 ENVELOPE GLYCOPROTEIN 120 VACCINES INHEALTHY THAI ADULTS,” J Infect Dis 188:219-227; Chuenchitra, T. et al.(2003) “LONGITUDINAL STUDY OF HUMORAL IMMUNE RESPONSES IN HIV TYPE 1SUBTYPE CRF01_AE (E)-INFECTED THAI PATIENTS WITH DIFFERENT RATES OFDISEASE PROGRESSION,” AIDS Res Hum Retroviruses 19:293-305; Schwartz, D.H. et al. (1995) “UTILITY OF VARIOUS COMMERCIALLY AVAILABLE HUMANIMMUNODEFICIENCY VIRUS (HIV) ANTIBODY DIAGNOSTIC KITS FOR USE INCONJUNCTION WITH EFFICACY TRIALS OF HIV-1 VACCINES,” Clin Diagn LabImmunol 2, 268-271). This will have a negative impact on futureprophylactic vaccine trials, in which early detection of HIV infectionsis of paramount importance. Furthermore, long-term HIV seropositivitywill exclude vaccine trial participants from the pool of blood andplasma donors, and will contribute to a plethora of socio-economic harmsincluding denied employment, health insurance, travel, immigration, andrecruitment to the armed forces (Belshe, R. B. et al. (1994)“INTERPRETING HIV SERODIAGNOSTIC TEST RESULTS IN THE 1990S: SOCIAL RISKSOF HIV VACCINE STUDIES IN UNINFECTED VOLUNTEERS,” NIAID AIDS VaccineClinical Trials Group. Ann Intern Med 121:584-589; Allen, M. et al.(2001) “TRIAL-RELATED DISCRIMINATION IN HIV VACCINE CLINICAL TRIALS.AIDS RES HUM RETROVIRUSES,” 17:667-674). Therefore, the prospect ofseroconversion could deter potential trial participants and severelycurtail recruitment into large scale trials around the globe (Gross, M.et al. (1996) “INTEREST AMONG GAY/BISEXUAL MEN IN GREATER BOSTON INPARTICIPATING IN CLINICAL TRIALS OF PREVENTIVE HIV VACCINES,” J AcquirImmune Defic Syndr Hum Retrovirol 12:406-412; Sheon, A. R. et al. (1998)“PREVENTING DISCRIMINATION AGAINST VOLUNTEERS IN PROPHYLACTIC HIVVACCINE TRIALS: LESSONS FROM A PHASE II TRIAL,” J Acquir Immune DeficSyndr Hum Retrovirol 19:519-526; Koblin, B. A. et al. (1998) “READINESSOF HIGH-RISK POPULATIONS IN THE HIV NETWORK FOR PREVENTION TRIALS TOPARTICIPATE IN HIV VACCINE EFFICACY TRIALS IN THE UNITED STATES,” Aids12:785-793. Currently, there is no HIV detection assay thatdifferentiates between vaccine generated antibodies and those producedafter true HIV infection during HIV vaccine trials.

HIV-2 (also known as the West African AIDS Virus) is closely related tothe simian immunodeficiency virus, and infected individuals are foundprimarily in West Africa (Smith, R. S. et al. (1990) “SYNTHETIC PEPTIDEASSAYS TO DETECT HUMAN IMMUNODEFICIENCY VIRUS TYPES 1 AND 2 INSEROPOSITIVE INDIVIDUALS,” Arch Pathol Lab Med. 114(3):254-258; Baillou,A. et al. (1991) “FINE SEROTYPING OF HUMAN IMMUNODEFICIENCY VIRUSSEROTYPE 1 (HIV-1) AND HIV-2 INFECTIONS BY USING SYNTHETIC OLIGOPEPTIDESREPRESENTING AN IMMUNODOMINANT DOMAIN OF HIV-1 AND HIV-2/SIMIANIMMUNODEFICIENCY VIRUS,” J Clin Microbiol. 29(7):1387-1391).

HIV acts to compromise the immune system of infected individuals bytargeting and infecting the CD-4⁺ T lymphocytes that would otherwise bethe major proponents of the recipient's cellular immune system response(Dalgleish, A. et al. (1984) “THE CD4 (T4) ANTIGEN IS AN ESSENTIALCOMPONENT OF THE RECEPTOR FOR THE AIDS RETROVIRUS,” Nature 312: 767-768,Maddon et al. (1986) “THE T4 GENE ENCODES THE AIDS VIRUS RECEPTOR AND ISEXPRESSED IN THE IMMUNE SYSTEM AND THE BRAIN,” Cell 47:333-348;McDougal, J. S. et al. (1986) “BINDING OF HTLV-III/LAV TO T4+ T CELLS BYA COMPLEX OF THE 110K VIRAL PROTEIN AND THE T4 MOLECULE,” Science231:382-385). HIV infection is pandemic and HIV-associated diseasesrepresent a major world health problem.

Infection of cells by HIV-1 requires membrane attachment of the virionand subsequent fusion of the viral and cellular membranes. The fusionprocess is mediated by the viral outer envelope glycoprotein complex(gp120/gp41) and target cell receptors (McGaughey, G. B. et al. (2004)“PROGRESS TOWARDS THE DEVELOPMENT OF A HIV-1 GP41-DIRECTED VACCINE,”Curr HIV Res. 2(2):193-204). The envelope glycoprotein is synthesized asa precursor protein (gp160) that is proteolytically cleaved into twonon-covalently associated protein subunits, a surface subunit (gp120)and a transmembrane subunit (gp41). The gp120 envelope protein isresponsible for binding to the CD4 cell-surface receptor and a chemokineco-receptor, CCRS or CXCR4. Following receptor binding, themembrane-anchored gp41 mediates fusion of the viral and target cellmembranes. The gp41 ectodomain contains a hydrophobic, glycine-richfusion peptide (amino acids 512-527) at the amino terminus that isessential for membrane fusion (numbering based on HXB2 gp160 variant asdescribed in Chan, D. C. et al. (1997) “CORE STRUCTURE OF GP41 FROM THEHIV ENVELOPE GLYCOPROTEIN,” Cell 89(2):263-273). Two 4,3 hydrophobicrepeat regions following the fusion peptide are defined by a heptadrepeat (abcdefg)n, where the residues occupying the a and d positionsare predominantly hydrophobic. The two heptad repeat regions arereferred to as the N36 (residues 546-581) and C34 (residues 628-661)peptides. A loop region containing a disulfide linkage separates the twoheptad repeat regions. The region of the gp41 ectodomain proximal to theviral membrane is abundant in the amino acid tryptophan (amino acids665-683) and has been shown to be critical for the membrane fusionmechanism of HIV-1. Gp41 exists in two distinct conformations, a nativeor non-fusogenic state and a fusion-active state (fusogenic state)(McGaughey, G. B. et al. (2004) “PROGRESS TOWARDS THE DEVELOPMENT OF AHIV-1 GP41-DIRECTED VACCINE,” Curr HIV Res. 2(2):193-204). On thesurface of free virions, gp41 exists in the native state with theN-terminal fusion peptide largely inaccessible. Following interaction ofthe gp120/gp41 complex with cell-surface receptors, gp41 undergoes aseries of conformational changes leading to the fusion-activeconformation (Chan, D. C. et al. (1998) HIV ENTRY AND ITS INHIBITION,”Cell 93(5):681-684). The transition from the native non-fusogenic tofusion-competent state proceeds through a nascent species termed theprehairpin intermediate. In this transient conformation, the N- andC-terminal regions of gp41 become separated; the N-terminal fusionpeptide is inserted into the target cell membrane and the C-terminalregion is anchored to the viral membrane. The prehairpin intermediateultimately folds into the fusion-active conformation bringing the viraland target membranes into proximity allowing viral entry into the targetcell (Chan, D. C. et al. (1998) HIV ENTRY AND ITS INHIBITION,” Cell93(5):681-684).

The detection of HIV infection may be accomplished by either identifyingviral proteins in the sera of infected individuals, by identifying viralnucleic acids in plasma or cells, or by detecting host antibodies thatare produced by such individuals in response to viral infection.Strategies involving the detection of viral proteins are complicated bythe low levels of such proteins during HIV infection, and by high assaycost. Thus, the detection of HIV infection is typically accomplished bydetecting host anti-HIV antibodies (Manocha, M. et al. (2003) “COMPARINGMODIFIED AND PLAIN PEPTIDE LINKED ENZYME IMMUNOSORBENT ASSAY (ELISA) FORDETECTION OF HUMAN IMMUNODEFICIENCY VIRUS TYPE-1 (HIV-1) AND TYPE-2(HIV-2) ANTIBODIES,” Immunol Lett. 85(3):275-278). Such detection ishowever, complicated by the etiology of HIV infection, in which asignificant initial “eclipse” period precludes detection of elicitedantibodies (Mortimer, P. P. (1991) “THE FALLIBILITY OF HIV WESTERNBLOT,” Lancet 11:286-286), and by persistent false positive results(Gnann, J. W. Jr. et al. (1989) “CUSTOM-DESIGNED SYNTHETIC PEPTIDEIMMUNOASSAYS FOR DISTINGUISHING HIV TYPE 1 AND TYPE 2 INFECTIONS ,”Methods Enzymol. 178:693-714). Due to these problems, more sensitive andexpensive tests, such as the Western blot are often needed to confirmpositive screening test results or to detect low level of circulatingvirus. However, Western blot analyses sometimes give indeterminateresults so that a combination of screening tests (ELISA or Rapid tests)is required to confirm the diagnosis (Mortimer, P. P. (1991) “THEFALLIBILITY OF HIV WESTERN BLOT,” Lancet 11:286-286; Brattegaard, K. etal. (1995) “INSENSITIVITY OF A SYNTHETIC PEPTIDE-BASED TEST (PEPTI-LAV1-2) FOR THE DIAGNOSIS OF HIV INFECTION IN AFRICAN CHILDREN ,” AIDS9(6):656-657). Additionally, different HIV proteins are expressed atdifferent times during infection. For example, the env-gene products ofHIV have been found to induce an immune response that precedes theimmune response of HIV's gag-related gene products (Döpel, S. H. et al.(1991) “COMPARISON OF FOUR ANTI-HIV SCREENING ASSAYS WHICH BELONG TODIFFERENT TEST GENERATIONS ,” Eur. J. Clin. Chem. Clin. Biochem.29:331-337).

The most common screening method for the diagnosis of infection withhuman immunodeficiency virus (HIV) is the detection (by sandwich ELISA)of virus-specific antibodies elicted by infected individuals in responseto the infection (Döpel, S. H. et al. (1991) “COMPARISON OF FOURANTI-HIV SCREENING ASSAYS WHICH BELONG TO DIFFERENT TEST GENERATIONS,”Eur. J. Clin. Chem. Clin. Biochem. 29:331-337; Manocha, M. et al. (2003)“COMPARING MODIFIED AND PLAIN PEPTIDE LINKED ENZYME IMMUNOSORBENT ASSAY(ELISA) FOR DETECTION OF HUMAN IMMUNODEFICIENCY VIRUS TYPE-1 (HIV-1) ANDTYPE-2 (HIV-2) ANTIBODIES ,” Immunol Lett. 85(3):275-278; Alcaro, M. C.et al. (2003) “SYNTHETIC PEPTIDES IN THE DIAGNOSIS OF HIV INFECTION ,”Curr Protein Pept Sci. 4(4):285-290; Beristain, C. N. et al. (1995)“EVALUATION OF A DIPSTICK METHOD FOR THE DETECTION OF HUMANIMMUNODEFICIENCY VIRUS INFECTION ,” J. Clin. Lab. Anal. 9(6):347-350).“First generation” assays used purified viral proteins obtained frominfected cells to bind, and identify, such antibodies. However, sincediagnostically relevant viral proteins, such as those encoded by theHIV-1 env gene were difficult to obtain in large quantities, “secondgeneration” assays were soon developed that employed recombinantlyproduced HIV antigens.

Unfortunately, the use of such recombinant products requires extensiveprotein purification in order to avoid false positive results. Thus, ithas been proposed that synthetic peptides be used to bind to and detectHIV-1 antibodies (Döpel, S. H. et al. (1991) “COMPARISON OF FOURANTI-HIV SCREENING ASSAYS WHICH BELONG TO DIFFERENT TEST GENERATIONS,”Eur. J. Clin. Chem. Clin. Biochem. 29:331-337; Manocha, M. et al. (2003)“COMPARING MODIFIED AND PLAIN PEPTIDE LINKED ENZYME IMMUNOSORBENT ASSAY(ELISA) FOR DETECTION OF HUMAN IMMUNODEFICIENCY VIRUS TYPE-1 (HIV-1) ANDTYPE-2 (HIV-2) ANTIBODIES,” Immunol Lett. 85(3):275-278; Alcaro, M. C.et al. (2003) “SYNTHETIC PEPTIDES IN THE DIAGNOSIS OF HIV INFECTION,”Curr Protein Pept Sci. 4(4):285-290; Baillou, A. et al. (1991) “FINESEROTYPING OF HUMAN IMMUNODEFICIENCY VIRUS SEROTYPE 1 (HIV-1) AND HIV-2INFECTIONS BY USING SYNTHETIC OLIGOPEPTIDES REPRESENTING ANIMMUNODOMINANT DOMAIN OF HIV-1 AND HIV-2/SIMIAN IMMUNODEFICIENCY VIRUS,”J Clin Microbiol. 29(7):1387-1391; Gnann, J. W. Jr. et al. (1989)“CUSTOM-DESIGNED SYNTHETIC PEPTIDE IMMUNOASSAYS FOR DISTINGUISHING HIVTYPE 1 AND TYPE 2 INFECTIONS,” Methods Enzymol. 178:693-714; Beristain,C. N. et al. (1995) “EVALUATION OF A DIPSTICK METHOD FOR THE DETECTIONOF HUMAN IMMUNODEFICIENCY VIRUS INFECTION,” J Clin Lab Anal. 1995;9(6):347-350; Modrow, S. et al. (1989) “CARRIER BOUND SYNTHETICOLIGOPEPTIDES IN ELISA TEST SYSTEMS FOR DISTINCTION B ETWEEN HIV-1 ANDHIV-2 INFECTION,” J Acquir Immune Defic Syndr. 2(2):141-148; Smith, R.S. et al. (1990) “SYNTHETIC PEPTIDE ASSAYS TO DETECT HUMANIMMUNODEFICIENCY VIRUS TYPES 1 AND 2 IN SEROPOSITIVE INDIVIDUALS,” ArchPathol Lab Med. 114(3):254-258).

Synthetic peptide antigens coupled with ELISA offers several potentialadvantages over other types of assays, potentially increasing thesensitivity and specificity of the assay, decreasing its cost, andproviding a relatively simple format that would be suitable for testingsizeable number of samples in any laboratory (Manocha, M. et al. (2003)“COMPARING MODIFIED AND PLAIN PEPTIDE LINKED ENZYME IMMUNOSORBENT ASSAY(ELISA) FOR DETECTION OF HUMAN IMMUNODEFICIENCY VIRUS TYPE-1 (HIV-1) ANDTYPE-2 (HIV-2) ANTIBODIES,” Immunol Lett. 85(3):275-278). Additionally,such peptides, if they elicit antibody formation, could be used as ananti-HIV vaccine (Petrov, R. V. et al. (1990) “THE USE OF SYNTHETICPEPTIDES IN THE DIAGNOSIS OF HIV INFECTIONS,” Biomed Sci. 1(3):239-244).

Suitable synthetic peptides comprise short protein sequences that can berecognized by antibodies that have been elicited through an individual'sexposure to the intact viral protein (Alcaro, M. C. et al. (2003)“SYNTHETIC PEPTIDES IN THE DIAGNOSIS OF HIV INFECTION,” Curr ProteinPept Sci. 4(4):285-290). In particular, it has been proposed that suchpeptides must possess the following characteristics: (1) an ability todetect an antibody response in all HIV-infected individuals; (2) anability to detect an antibody response as early as possible afterinfection; and (3) an ability to maintain detection of antibody responseover all stages of the disease (Döpel, S. H. et al. (1991) “COMPARISONOF FOUR ANTI-HIV SCREENING ASSAYS WHICH BELONG TO DIFFERENT TESTGENERATIONS,” Eur. J. Clin. Chem. Clin. Biochem. 29:331-337; Döpel, S.H. et al. (1990) “FINE MAPPING OF AN IMMUNODOMINANT REGION OF THETRANSMEMBRANE PROTEIN OF THE HUMAN IMMUNODEFICIENCY VIRUS (HIV-1),” J.Virol. Meth. 25:167-178; Alcaro, M. C. et al. (2003) “SYNTHETIC PEPTIDESIN THE DIAGNOSIS OF HIV INFECTION,” Curr Protein Pept Sci.4(4):285-290). In particular, the HIV-1 p24 (gag) protein, gp160/120(env) protein and gp41 (env envelope transmembrane protein) have beenproposed as having serodiagnostic importance, and as being a potentialsource of suitable peptides (Alcaro, M. C. et al. (2003) “SYNTHETICPEPTIDES IN THE DIAGNOSIS OF HIV INFECTION,” Curr Protein Pept Sci.4(4):285-290).

Additionally, it is important to be able to distinguish between theHIV-1 and HIV-2 variants of HIV (Smith, R. S. et al. (1990) “SYNTHETICPEPTIDE ASSAYS TO DETECT HUMAN IMMUNODEFICIENCY VIRUS TYPES 1 AND 2 INSEROPOSITIVE INDIVIDUALS,” Arch Pathol Lab Med. 114(3):254-258; Baillou,A. et al. (1991) “FINE SEROTYPING OF HUMAN IMMUNODEFICIENCY VIRUSSEROTYPE 1 (HIV-1) AND HIV-2 INFECTIONS BY USING SYNTHETIC OLIGOPEPTIDESREPRESENTING AN IMMUNODOMINANT DOMAIN OF HIV-1 AND HIV-2/SIMIANIMMUNODEFICIENCY VIRUS,” J Clin Microbiol. 29(7):1387-1391; Modrow, S.et al. (1989) “CARRIER BOUND SYNTHETIC OLIGOPEPTIDES IN ELISA TESTSYSTEMS F OR DISTINCTION BETWEEN HIV-1 AND HIV-2 INFECTION,” J AcquirImmune Defic Syndr. 2(2):141-148). These variants share 40-60% homologyat the amino acid level (Alcaro, M. C. et al. (2003) “SYNTHETIC PEPTIDESIN THE DIAGNOSIS OF HIV INFECTION,” Curr Protein Pept Sci. 4(4):285-290;Gueye-Ndiaye, A. et al. (1993) “COST-EFFECTIVE DIAGNOSIS OF HIV-1 ANDHIV-2 BY RECOMBINANT-EXPRESSED ENV PEPTIDE (566/996) DOT-BLOT ANALYSIS,”AIDS. 7(4):475-481).

Methods for detecting HIV or other viral pathogens are disclosed inWO9008162A1, and in U.S. Pat. Nos: 6,689,879; 6,649,749; 6,623,920;6,589,734; 6,586,177; 6,582,920; 6,541,609; 6,534,285; 6,531,276;6,492,104; 6,458,527; 6,399,307; 6,352,826; 6,270,959; 6,252,059;6,245,737; 6,048,685; 6,008,044; 5,928,642; 5,925,513; 5,891,623;5,856,088; 5,849,494; 5,830,641; 5,721,095; 5,712,385; 5,705,331;5,695,930; 5,681,696; 5,660,979; 5,637,453; 5,599,662; 5,476,765;5,462,852; 5,459,060; 5,260,189; and in European Patent DocumentsEP0439077B1, EP0439077A2.

Substantial progress has been made in the management and treatment ofHIV-1 infection. However, available antiretroviral therapies can causemetabolic toxicity (Sommerfelt, M. A. et al. (2004) “NOVEL PEPTIDE-BASEDHIV-1 IMMUNOTHERAPY,” Expert Opin Biol Ther. 4(3):349-61), and thusalternative strategies to control HIV-1 infection are needed (McGaughey,G. B. et al. (2004) “PROGRESS TOWARDS THE DEVELOPMENT OF A HIV-1GP41-DIRECTED VACCINE,” Curr HIV Res. 2(2):193-204). The use of peptideimmunogens has been proposed as the basis for an anti-HIV-1 vaccine(Sommerfelt, M. A. et al. (2004) “NOVEL PEPTIDE-BASED HIV-1IMMUNOTHERAPY,” Expert Opin Biol Ther. 4(3):349-61; Berzofsky, J. A. etal. (1995) “NOVEL APPROACHES TO PEPTIDE AND ENGINEERED PROTEIN VACCINE SFOR HIV USING DEFINED EPITOPES: ADVANCES IN 1994-1995,” AIDS 9 SupplA:S143-157; Choppin, J. et al. (2001) “CHARACTERISTICS OF HIV-1 NEFREGIONS CONTAINING MULTIPLE CD8+ T CELL EPITOPES: WEALTH OF HLA-BINDINGMOTIFS AND SENSITIVITY TO PROTEASOME DEGRADATION,” J. Immunol.166(10):6164-6169; Berzofsky, J A. et al. (1999) “APPROACHES TO IMPROVEENGINEERED VACCINE S FOR HUMAN IMMUNODEFICIENCY VIRUS AND OTHER VIRUSESTHAT CAUSE CHRONIC INFECTIONS,” Immunol Rev. 170:151-172; Cho, M. W.(2003) “SUBUNIT PROTEIN VACCINE S: THEORETICAL AND PRACTICALCONSIDERATIONS FOR HIV-1,” Curr Mol. Med. 3(3):243-263; Sabatier, J. M.et al. (1989) “USE OF SYNTHETIC PEPTIDES FOR THE DETECTION OF ANTIBODIESAGAINST THE NEF REGULATING PROTEIN IN SERA OF HIV-INFECTED PATIENTS,”AIDS. 3(4):215-220; van der Ryst, E. (2002) “PROGRESS IN HIV VACCINERESEARCH,” Oral Dis. 8 Suppl 2:21-26; Zolla-Pazner, S. (2004)“IDENTIFYING EPITOPES OF HIV-1 THAT INDUCE PROTECTIVE ANTIBODIES,” NatRev Immunol. 4(3):199-210.

Unfortunately, the identification of suitable peptides is encumbered bythe rapid mutation and recombination exhibited by retroviruses, extremevariability is found in HIV proteins. Although conserved regions inHIV-1 gp120 (residues 495-516), gp41 (residues 67-83 and 584-618), andgp36 (residues 574-602) have been investigated as potential sequencesfor candidate peptides (Alcaro, M. C. et al. (2003) “SYNTHETIC PEPTIDESIN THE DIAGNOSIS OF HIV INFECTION,” Curr Protein Pept Sci.4(4):285-290), prior efforts to define suitable peptides have not beenfully satisfactory. Petrov, R. V. et al. disclose that many candidatepeptides failed to identify HIV infection in HIV-infected individuals,necessitating the use of multiple peptides in order to detect HIVinfection (Petrov, R. V. et al. (1990) “THE USE OF SYNTHETIC PEPTIDES INTHE DIAGNOSIS OF HIV INFECTIONS,” Biomed Sci. 1(3):239-244). Thus, animportant problem facing the field of HIV diagnostics is theidentification of a suitable peptide that would be recognized broadly,or universally, by the full range of clinically identified HIV variants.Likewise, at present no identified peptide has resulted in an HIV-1immunotherapy that could be used as the basis for a vaccine that wouldprovide substantial or full immunoprotection to infection by suchvariants (Sommerfelt, M. A. et al. (2004) “NOVEL PEPTIDE-BASED HIV-1IMMUNOTHERAPY,” Expert Opin Biol Ther. 4(3):349-61). In addition,suitable diagnostic tests should be able to distinguish betweenindividuals whose sera contain anti-HIV antibodies as a result of theirreceipt of an anti-HIV vaccine and individuals whose sera containanti-HIV antibodies as a result of HIV infection. The present inventionis directed to this and other needs.

SUMMARY OF THE INVENTION

This invention relates to compositions and methods for the detection ofimmunodeficiency virus infection, especially human immunodeficiencyvirus-1 (HIV-1) and human immunodeficiency virus-2 (HIV-2) infection.The invention particularly concerns compositions and methods that may beused in HIV vaccine recipients whose sera may contain vaccine-generatedanti-HIV antibodies. The invention also concerns peptide antigens thatmay be used in anti-HIV vaccine compositions.

Most of the HIV-1 prophylactic vaccines currently under development arecomplex products containing multiple viral genes or proteins. As aresult, vaccine recipients' sera are expected to be identified asreactive in HIV-1 or HIV-2 or both HIV 1 & 2 seroconversion detectionassays and thus to produce patterns indistinguishable form sera obtainedfrom infected individuals. This will have a negative impact on futureclinical trials of prophylactic HIV vaccines that require earlydetection of breakthrough infections. It will also exclude all vaccinesfrom the pool of potential blood donors, and may contribute to othersocial harms. The present invention is directed, in part, to theidentification of new HIV-1 and HIV-2 epitopes which are: (a) broadlyreactive with early serum samples from individuals infected with HIVvirus strains from all clades; (b) do not contain protective antibody orcytotoxic epitopes; and (c) can be easily removed from current andfuture HIV-1 candidates. In a preferred embodiment, Gene-Fragment PhageDisplay libraries constructed from whole HIV-1 genome are used toidentify such epitopes and to construct differential enzyme-immunoassaysthat are capable of distinguishing reactivities from infection-inducedanti-HIV antibodies from vaccine-induced anti-HIV reactivities.

In one aspect, the invention relates to a method for detecting thepresence, or measuring the concentration, of an anti-HIV-1 antibody in abiological sample of a human, wherein said method comprises conductingan immunoassay comprising the steps of: (a) contacting said biologicalsample with a peptide having an epitope that is recognized by saidanti-HIV-1 antibody, said contacting being under conditions sufficientto permit said anti-HIV-1 antibody if present in said sample to bind tosaid epitope and form a peptide-anti-HIV-1 antibody complex; (b)contacting said formed peptide-anti-HIV-1 antibody complex with ananti-HIV-1 antibody binding molecule, said contacting being underconditions sufficient to permit said anti-HIV-1 antibody bindingmolecule to bind to anti-HIV-1 antibody of said formedpeptide-anti-HIV-1 antibody complex and form an extended complex; and(c) determining the presence or concentration of said anti-111V-1antibody in said biological sample by determining the presence orconcentration of said formed extended complex; wherein said epitope ispresent on a peptide having an amino acid sequence selected from thegroup consisting of SEQ ID NOs:1-11, 49-56, 90 and 141.

In another aspect, the invention relates to a a peptide or proteincomprising an epitope that is recognized by an anti-HIV-1 antibody,wherein said epitope is present on a peptide having the amino acidsequence of SEQ ID NO:3, SEQ ID NO:50, SEQ ID NO:55 or SEQ ID NO:141.

In another aspect, the invention relates to a peptide or protein havingthe amino acid sequence of SEQ ID NO:3, SEQ ID NO:50, SEQ ID NO:55 orSEQ ID NO:141.

In another aspect, the invention relates to an immunological complexcomprising a peptide bound to an anti-HIV-1 antibody, wherein saidanti-HIV-1 antibody is additionally bound to an anti-HIV antibodybinding molecule, wherein said peptide or protein comprises an epitopethat is recognized by an anti-HIV-1 antibody, said epitope being presenton a peptide or protein having an amino acid sequence selected from thegroup consisting of SEQ ID NOs:1-11, 49-56, 90 and 141.

In a further aspect, the invention relates to a kit for detecting thepresence, or measuring the concentration, of an anti-HIV-1 antibody in abiological sample of a human, wherein said kit comprises a hollow casingcomprising a multilayer filter system, and first and second porouscarriers, wherein said second porous carrier is in communication withsaid first porous carrier, and said first porous carrier is incommunication with said multilayer filter system, a portion of which isaccessible from said casing; wherein said first porous carrier containsa non-immobilized, labeled peptide or protein; and said second porouscarrier contains an immobilized, unlabeled antibody that binds to humanIgG; wherein said peptide or protein comprises an epitope that ispresent on a peptide having an amino acid sequence selected from thegroup consisting of SEQ ID NOs:1-11, 49-56, 90 and 141.

In a further aspect, the invention relates to a method for detecting thepresence, or measuring the concentration, of an anti-HIV-2 antibody in abiological sample of a human, wherein said method comprises conductingan immunoassay comprising the steps of: (a) contacting said biologicalsample with a peptide having an epitope that is recognized by saidanti-HIV-2 antibody, said contacting being under conditions sufficientto permit said anti-HIV-2 antibody if present in said sample to bind tosaid epitope and form a peptide-anti-HIV-2 antibody complex; (b)contacting said formed peptide-anti-HIV-2 antibody complex with ananti-HIV-2 antibody binding molecule, said contacting being underconditions sufficient to permit said anti-HIV-2 antibody bindingmolecule to bind to anti-HIV-2 antibody of said formedpeptide-anti-HIV-2 antibody complex and form an extended complex; and(c) determining the presence or concentration of said anti-HIV-2antibody in said biological sample by determining the presence orconcentration of said formed extended complex; wherein said epitope ispresent on a peptide having an amino acid sequence selected from thegroup consisting of SEQ ID NOs:101-102.

In another aspect, the invention relates to a method for detecting thepresence, or measuring the concentration, of an anti-HIV-1 antibody in abiological sample of a human, wherein said method comprises conductingan immunoassay comprising the steps of: (a) contacting said biologicalsample with an epitope set comprising at least one epitope that isrecognized by said anti-HIV-1 antibody, wherein said epitope setconsists essentially of an HIV-1 GAG p6 epitope or epitopes, an HIV-1gp41 terminal region epitope or epitopes, or a combination of an HIV-1GAG p6 epitope or epitopes and an HIV-1 gp41 terminal region epitope orepitopes, said contacting being under conditions sufficient to permitsaid anti-HIV-1 antibody if present in said sample to bind to epitopesin said epitope set and form an epitope-anti-HIV-1 antibody complex; (b)contacting said formed epitope-anti-HIV-1 antibody complex with ananti-HIV-1 antibody binding molecule, said contacting being underconditions sufficient to permit said anti-HIV-1 antibody bindingmolecule to bind to anti-HIV-1 antibody of said formedepitope-anti-HIV-1 antibody complex and form an extended complex; and(c) determining the presence or concentration of said anti-HIV-1antibody in said biological sample by determining the presence orconcentration of said formed extended complex.

In a further aspect, the invention relates to a method for detecting thepresence, or measuring the concentration, of an anti-HIV-2 antibody in abiological sample of a human, wherein said method comprises conductingan immunoassay comprising the steps of: (a) contacting said biologicalsample with an epitope set comprising at least one epitope that isrecognized by said anti-HIV-2 antibody, wherein said epitope setconsists essentially of an HIV-2 GAG p6 epitope or epitopes, an HIV-2Env-gp36 epitope or epitopes, or a combination of an HIV-2 GAG p6epitope or epitopes and an HIV-2 Env-gp36 epitope or epitopes, saidcontacting being under conditions sufficient to permit said anti-HIV-2antibody if present in said sample to bind to epitopes in said epitopeset and form an epitope-anti-HIV-2 antibody complex; (b) contacting saidformed epitope-anti-HIV-2 antibody complex with an anti-HIV-2 antibodybinding molecule, said contacting being under conditions sufficient topermit said anti-HIV-2 antibody binding molecule to bind to anti-HIV-1antibody of said formed epitope-anti-HIV-1 antibody complex and form anextended complex; and (c) determining the presence or concentration ofsaid anti-HIV-2 antibody in said biological sample by determining thepresence or concentration of said formed extended complex.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 shows a general scheme for constructing the gene fragment phagedisplay libraries used in a preferred embodiment of the invention toobtain novel HIV epitopes.

FIG. 2 shows a general scheme for panning gene fragment phage displaylibraries.

FIG. 3 illustrates the relationship between the epitopes employed in HIVvaccines and those identified in the preferred embodiments of thepresent invention.

FIG. 4 shows the frequency of negative samples (n=600) obtained inELISAs employing the GAG-p6 (SEQ ID NO:3; Panel A) and gp41 (SEQ IDNO:50; Panel B) peptides.

FIG. 5, Panels a-d, shows the dynamic range of serum reactivity andreproducibility of the p6 (SEQ ID NO:3) and gp41 (SEQ ID NO:50 and SEQID NO:55) peptide-based HIV-SELECTEST. ELISA conditions were describedin Example 9, METHODS. A well characterized panel of nine HIVseropositive and three HIV seronegative human plasma (SeraCareBioServices) were subjected to serial two-fold dilutions starting at1:50. Reactivity of one of the seropositive samples, PRB-204-06, with p6(Panel a) and gp41 (Panel b) peptides is shown. Quality assurance dataobtained with p6 (Panel c) and gp41 (SEQ ID NO:50 and SEQ ID NO:55)(Panel d) demonstrate the reproducibility of the new assay. In thesepanels, the same plasma was tested on nine dates at a 1:100 dilution.All data are represented as ratios between test specimen optical density(OD) to cut-off absorbance (CO) on the Y-axis. The Cut-off value foreach peptide was determined as the mean absorbance+5 standard deviations(SD) obtained with 1000 HIV seronegative samples. The upper and lowerlimits (Panels c, d) are the average OD/CO values±2SD of the plasmasample upon repeated testing, representing the 95% confidence intervalsfor the given control sample. Data shown represents similar results withall nine plasma samples in the control panel.

FIG. 6 shows the seroreactivity of intercurrent HIV infections duringHIV vaccine trials. Reactivity in the HIV-SELECTEST of sequential plasmasamples obtained from intercurrent infections in the course of: (a)multiple phase I/II HIV vaccine trials conducted by the HVTN (15vaccinees and 4 placebos) and VRC 004 (2 placebos); (b) VAX 003 phaseIII trial in Thailand (30 vaccinees and 35 placebos); (c) VAX 004 phaseIII trial in the United States and the Netherlands (53 vaccinees and 28placebos). For each infected subject, multiple time points within 3months of estimated infection date (panel a) or confirmed infection byPCR (depicted as day 0 on Y-axis, panels b and c) are shown vertically.Open circles (◯) represent negative reactivity in the HIV-SELECTEST(OD/CO<1), and filled circles () represent positive reactivity in theHIV-SELECTEST (OD/CO≧1). Detailed reactivity data for all the samplestested are shown in Table 27, Table 29 and Table 30.

FIG. 7, Panels a and b shows comparative reactivity of early samplesfrom HIV infections during the VAX 003 (Thailand) and VAX 004 (UnitedStates and the Netherlands) clinical trials in the HIV-SELECTEST andlicensed HIV detection kits used in the VaxGen trials. Early sequentialsamples obtained from HIV infected vaccine trial participants in VAX 003(30 vaccinees and 35 placebos; Panel a) and VAX 004 (53 vaccinees and 28placebos; Panel b) were tested in the HIV-SELECTEST as described inMETHODS, and by VaxGen using licensed HIV diagnostic tests. Day 0represents the day of confirmed infection by qualitative PCR. Each dotin the figures represent the earliest bleed (post infection) on which agiven infected individual scored positive by the licensed HIV diagnostickits (X-axis) compared with the HIV-SELECTEST (Y-axis).

DESCRIPTION OF THE PREFERRED EMBODIMENTS

This invention relates to compositions and methods for the detection ofimmunodeficiency virus infection, especially immunodeficiency virus-1(HIV-1) infection. The invention particularly concerns compositions andmethods that may be used in HIV vaccine recipients whose sera maycontain vaccine-generated anti-HIV-1 antibodies.

Since 1987, more than 10,000 individuals have received immunizationswith human immunodeficiency virus (HIV) preventive vaccine constructs.Two large phase III trials are close to completion in the U.S. andThailand (8,000 vaccinees) and a new phase III trial is ongoing inThailand (16,000 vaccinees). Earlier vaccine candidates were simple andusually included a single gene product, such as the viral glycoproteingp120 or gp160. Most of the HIV-1 prophylactic vaccines currently underdevelopment are complex products containing multiple viral genes orproteins.

Unfortunately, despite such efforts, the HIV pandemic continues to takeits toll globally, with more than 16,000 reported infections and 8,500deaths occurring daily. Concerted efforts are underway to developpreventative HIV vaccines that will be both efficacious and economical.In the wake of the unsuccessful efficacy trials conducted with vaccinescontaining gp120 envelope alone (Francis, D. P. et al. (2003) “CANDIDATEHIV/AIDS VACCINE S: LESSONS LEARNED FROM THE WORLD′S FIRST PHASE IIIEFFICACY TRIALS,” Aids 17:147-56; Graham, B. S. et al. (2005) “LESSONSFROM FAILURE—PREPARING FOR FUTURE HIV-1 VACCINE EFFICACY TRIALS,” JInfect Dis 191, 647-649), the new generation of vaccine candidates arecomplex products, containing multiple HIV genes or proteins, usingdiverse delivery systems and new adjuvants. It is anticipated thatwithin few years several vaccine candidates will progress into largescale efficacy trials, particularly in countries with high infectionrates. It is hoped that the new generation vaccines will offer at leastpartial protection against new infections and possibly reduce viralloads and delay disease progression in infected vaccinated individuals.In order to achieve the statistical power needed to demonstrate partialefficacy, it will be necessary to recruit thousands of volunteers intofuture phase III HIV vaccine trials. Many of these volunteers will reactpositively in licensed HIV detection tests. Hence, further improvementsin HIV diagnosis are urgently required.

One of the critical determinations during ongoing trials in high-riskpopulations is the HIV infection status of trial participants.Intercurrent infections must be detected as soon as possible in order tostop vaccination and monitor infected individuals for viral load, immunestatus, and disease progression. Treatment and public health measuresdepend on a timely diagnostic information. Currently, vaccine trials areusing an algorithm of HIV detection that incorporates antibody orantigen-based kits, followed by Western Blots and finally, confirmatoryPCR based assays. Unfortunately, many of the vaccine trial participants,irrespective of their HIV infection status, seroconvert in all licensedantibody detection kits, including the recently licensed rapid tests((Ackers, M. L. et al. (2003) “HUMAN IMMUNODEFICIENCY VIRUS (HIV)SEROPOSITIVITY AMONG UNINFECTED HIV VACCINE RECIPIENTS,” J Infect Dis187:879-986; Pitisuttithum, P. et al. (2003) “SAFETY AND IMMUNOGENICITYOF COMBINATIONS OF RECOMBINANT SUBTYPE E AND B HUMAN IMMUNODEFICIENCYVIRUS TYPE 1 ENVELOPE GLYCOPROTEIN 120 VACCINE S IN HEALTHY THAIADULTS,” J Infect Dis 188:219-227; Chuenchitra, T. et al. (2003)“LONGITUDINAL STUDY OF HUMORAL IMMUNE RESPONSES IN HIV TYPE 1 SUBTYPECRF01_AE (E)-INFECTED THAI PATIENTS WITH DIFFERENT RATES OF DISEASEPROGRESSION,” AIDS Res Hum Retroviruses 19:293-305; Schwartz, D. H. etal. (1995) “UTILITY OF VARIOUS COMMERCIALLY AVAILABLE HUMANIMMUNODEFICIENCY VIRUS (HIV) ANTIBODY DIAGNOSTIC KITS FOR USE INCONJUNCTION WITH EFFICACY TRIALS OF HIV-1 VACCINE S,” Clin Diagn LabImmunol 2, 268-271). This is due to the fact that vaccine components arevery similar to the diagnostic kits in composition. Therefore,recruitment of volunteers into future trials may be impeded if theinformed consent forms state that volunteers are likely to seroconvertin licensed detection kits and may remain seropositive for a long time.In published surveys, it has been shown that positive HIV serodiagnosisis the most important concern for volunteers willing to participate inHIV clinical trials (Gross, M. et al. (1996) “INTEREST AMONGGAY/BISEXUAL MEN IN GREATER BOSTON IN PARTICIPATING IN CLINICAL TRIALSOF PREVENTIVE HIV VACCINE S,” J Acquir Immune Defic Syndr Hum Retrovirol12:406-412). Thus, there is an immediate need to develop a simple andinexpensive assay that does not score uninfected vaccine recipients aspositive, but provides the necessary specificity and sensitivity todetect true HIV infections in the presence of vaccine-inducedantibodies.

The systems used to deliver such vaccines span the gamut from plasmidDNA to viral and bacterial vectors. Prime-boost strategies have beenemployed in order to optimize the cellular and humoral immune responsesand reach meaningful (protective) titers and breadth of neutralizingantibodies and high frequency of cytotoxic T cells. Unfortunately, manyof these constructs elicit antibodies detected by standard serologictests for HIV-1 seroconversion. In a recent publication from the UnitedStates' Center for Disease control and Prevention, it was reported that90% of vaccinees receiving a Canarypox construct expressing multiple HIVgenes (env, gag, pol, protease, net) followed by an envelope proteinboost, exhibited positive results in an enzyme immunoassay (EIA), rapidtest, and Western blot (Marta-Louise Ackers et al. J. Infect. Dis. 2003,187:879).

Due to increasing complexity of HIV-1 vaccine candidates, most vaccineesare expected to react positive in the licensed HIV-1 detection assays(EIA, rapid test, Western blots). There are several negative outcomes tothe anticipated high prevalence of false-positives in the vaccinatedindividuals. These outcomes reflect the criticality of distinguishingbetween HIV infected recipients and individuals who have merely becomeseroconverted due to the administration of the vaccine:

-   -   (a) Phase III trials of prophylactic HIV-1 vaccines are        typically and desirably conducted in high risk populations. As        such, it is essential to diagnose break-through infections at        the earliest possible times. This is necessary since infected        individuals must stop vaccinations and get re-assigned to a        follow-up group that are analyzed separately. Additionally, such        individuals may be entitled to anti-viral therapies;    -   (b) Since HIV-1 infected individuals are excluded from the pool        of potential blood donors, it is important to ensure both that        infected individuals do not donate blood, and that individuals        who have merely become seroconverted due to the administration        of the vaccine are not erroneously precluded from serving as        blood donors.    -   (c) Since HIV-1 infected individuals face exclusions from health        insurance, immigration and travel across countries, employment        limitations, and preclusion from military service, it is        important to be able to ensure that healthy vaccine recipients        are not erroneously scored as HIV-infected individuals.    -   (d) Informing potential participants about the strong        possibility of having reactive serologic HIV-1 tests, could        deter potential volunteers from participating because of        anticipated social harms. Therefore, it is important to design        new testing strategies for vaccine participants that will        clearly discriminate between vaccine-induced reactivity and        HIV-1 infection.

The present invention addresses these concerns by providing new HIV-1epitopes that will fulfill some, and more preferably all, of thefollowing criteria:

-   -   (1) Do not contain important neutralizing or CTL epitopes;    -   (2) Are not present in HIV vaccine constructs;    -   (3) Arc highly immunogenic in infected individuals;    -   (4) Are recognized by antibodies from HIV infected individuals        at early times post-infection; and    -   (5) Are highly conserved among clades and subtypes.

Identification of the Novel Epitopes of the Present Invention

In order to identify epitopes that conform to the above criteria, it isdesirable to evaluate a large pool of potential epitopes.Advantageously, a gene-fragment phage display library may be employedfor this purpose. Preferably, such a library is produced using limitedDNase I digestion of HIV-1 or HIV-2 DNA (FIG. 1). Thus, target DNA,containing HIV-1 or HIV-2, is subjected to DNAse I digestion, and thedigestion products are fractionated, for example using gelelectrophoresis. The termini of the fractionated samples are preferablypolished using T4 polymerase (see, e.g., Costa, G. L. et al. (1994)“POLISHING WITH T4 OR PFU POLYMERASE INCREASES THE EFFICIENCY OF CLONINGOF PCR FRAGMENTS,” Nucleic Acids Res. 22(12):2423) and dephosphorylated.The treated fragments are then preferably introduced into a phagemid orphage vectors (based on filamentous phages including M13, f1, etc.)operably linked to a displayed phage protein and are then amplified toproduce a phage display library, each of whose members displays an HIVpeptide sequence on its surface. Alternatively, other libraries can beused including Ribosomal display, other viruses, and phages or bacterialcells or Yeast or other eukaryotic display systems for the same purpose.

Desired peptides are then identified, preferably by panning the libraryon immobilized serum antibodies from HIV-1-infected individual (earlyseroconversion) under conditions that permit the recovery of librarymembers that bind strongly to the immobilized antibodies (FIG. 2).Preferably, this is accomplished by capturing library members whosearrayed HIV peptide binds to an immobilized anti-HIV antibody. Afterdiscarding unbound phagemids, the bound phagemids are eluted andrecovered (eluted phagemids may be amplified to enhance their recovery).

Suitable members mapping to the HIV-1 GAG-p6, RT, IN, Vif, gp120, gp41,and Nef genes, for example, can be identified in this manner. Ofparticular interest are members mapping to the gag, pol, Envelope andnef encoding regions of HIV. Further screenings are preferably conductedusing panels of sequential sera from HIV-1 seroconvertors. FIG. 3illustrates the relationship between the desired epitopes of the presentinvention, and those of vaccine candidates.

Epitopes mapping to the HIV-1 GAG-p6, gp41, Vif and Nef genes arebelieved to possess significant utility as diagnostic agents for thedetection of anti-HIV antibodies, since, for gp41 and p6, there is >90%sequence conservation among HIV-1 clades. Moreover, gp41 and Gag-p6peptides were recognized at high frequency (combined sensitivity of99.1%) by serum/plasma of 1200 samples from seropositive individualsincluding early seroconvertors. The specificity is currently at 98.2%for p6 and 100% for gp41 (1000 negative samples). The Gag-p6 and gp41peptides do not contain important known neutralizing antibody or CTLepitopes and they are not present in most HIV vaccines. Identifiedpeptides are suitable for use in HIV diagnostic kits.

In particular, the following HIV-1 peptide Gag-p6 sequences wereidentified as comprising desired epitopes:

C-GAG-p6 (SEQ ID NO: 1)SRPEPTAPPA ESFRFGEEIT PTPSQKQEPK DKELYPPLAS LRSLFGNDPS SN1        10         20         30         40         50 52 GAG-p6(SEQ ID NO: 2) SRPEPTAPPE ESFRFGEETT TPSQKQEPID KELYPLASLR SLFGSDPSSQ1        10         20         30         40         50 CON-GAG-p6(SEQ ID NO: 3) SRPEPTAPPA ESFRFGEEIT PTPSQKQEPK DKELYPPLAS LRSLFGNDPS SQ1        10         20         30         40         50 52 CON-M-p6(SEQ ID NO: 4) SRPEPTAPPA ESFRFGEETT PSPKQEPKDK ELYPLTSLKS LFGNDPLSQ1        10         20         30         40         49 P6-CON-of-CON(SEQ ID NO: 5) SRPEPTAPPA ESFGFGEEIT PSPKQEPKDK ELYPLASLKS LFGNDPLSQ1        10         20         30         40         49 CON-p6 A > E(SEQ ID NO: 6) SRPEPTAPPE ESFRFGEEIT PTPSQKQEPK DKELYPPLAS LRSLFGNDPS SQ1        10         20         30         40         50 52 New -GAG-p6(SEQ ID NO: 7) SRPEPTAPPE ESFRFGEEIT PTPSQKQEPK DKELYPLASL RSLFGNDPSS  Q1        10         20         30         40         50 51 p6-S-S(SEQ ID NO: 8) SRPEPTAPPA ESFRFGEEIT TSPSQKQEPK DKELYPLASL KSLFGND1        10         20         30         40      47 p6-S-E(SEQ ID NO: 9) SRPEPTAPPA ESFRFGEEIT TSPSQKQEPK DKE1        10         20         30  33 p6-T-S (SEQ ID NO: 10)TPTPSQKQEP KDKELYPPLA SLRSLFGNDP  S 1        10         20         30 31p6-S-Q (SEQ ID NO: 11) SFRFGEEITP TPSQKQEPKD KELYPPLASL  RSLFGNDPSS Q1        10         20         30 31

Each of these sequences was attached individually to a carboxy-terminal(SEQ ID NO: 138) GGGC peptide linker.

Identified GAG Epitopes

The identified GAG epitopes (SEQ ID NOs:1-11) differ in sequence fromthe sequences of previously identified GAG peptides. For example,aligning SEQ ID NO:1 and SEQ ID NO:2 against the HIV-1 GAG sequence (SEQID NO:12; NC_(—)001802) yields the following comparison (sites of SEQ IDNO:12 that are not conserved are shown in single-underline (if conservedin either SEQ ID NO:1 or SEQ ID NO:2) or in double-underline (if notconserved in either SEQ ID NO:1 or SEQ ID NO:2)) (Table 1):

TABLE 1 SEQ ID NO Description Sequence  1 Isolated EpitopeSRPEPTAPPAESFRFGEEITPTPSQKQEPKDKELYPPLASLRSLFGNDPSSN  2 Isolated EpitopeSRPEPTAPPEESFRFGEETT•TPSQKQEPIDKELYP•LASLRSLFGSDPSSQ 12 GagSRPEPTAPPEESFRSGVETT•TPPQKQEPIDKELYP•LTSLRSLEGNDPSSQ

Thus, both SEQ ID NO:1 and SEQ ID NO:2 differ in sequence from thesequence of the corresponding native HIV-1 gag gene product (SEQ IDNO:12). An alignment of these sequences with a series of gag consensussequences (Table 2) indicates that SEQ ID NO:1 and SEQ ID NO:2 differ insequence from the consensus sequences. The “$” symbol in Table 2indicates a stop codon.

TABLE 2 SEQ ID NO Description Sequence 12 GagSRPEPTAPPEESFRSGVET•T•TPPQKQEPIDKE•LYP•LTSLRSLFGNDPSSQ  1Isolated Epitope SRPEPTAPPAESFRFG•EI•TPTPSQKQEPKDKE•LYPPLASLRSLFGNDPSSN 2 Isolated EpitopeSRPEPTAPPEESFRFG•E••TTTPSQKQEPIDKE•LYP•LASLRSLFGSDPSSQ 13 Consensus_BSRPEPTAPPEESFRFG•EE•TTTPSQKQEPIDKE•LYP•LASLRSLFGNDPSSQ (33) 14Consensus_02(8) SRPEPTAPPAESFGMG•EEIT••SSPKQEPRDKG•LYPPLASLKSLFGNDP$SQ15 Consensus_D(8) SRPEPTAPPAESFGFG•EEIT••PSQKQEQKDKE•LYP•LTSLKSLFGNDPLSQ16 Consensus F1- NRPEPTAPPAESFGFR•EEIT••PSPKQEQKD•EGLYPPLASLKSLFGNDP•••F2(9) 17 Consensus_G(5)NRPEPTAPPAESFGFG•EEIA••PSPKQEQKEKE•LYP•LASLKSLFGSDP$SQ 18Consensus_K (3) SRPEPTAPPAESFGFG•EEITP••SPRQETKDKE•QGPPLTSLKSLFGNDPLSQ19 Consensus_A- SRPEPTAPPAEIFGMG•EEITS••PPKQEQKDRE•QNPPSVSLKSLFGNDPLSQA1-A2(15) 20 Consensus_H (3)SRPEPTAPPAESFGFG•EEMT••PSPKQELKDKE•••PPLASLRSLFGNDPLSQ 21 Consensus_01SRPEPTAPPAENGMGE•E•ITSLP••KQEQKDKE•HPPPLVSLKSLFGNDPLSQ (11) 22Consensus_c (41) SRPEPTAPPAESFRF••EE•T•TPAPKQEPKDRE••••PLTSLKSLFGSDPLSQ

The invention also relates to the following HIV 1 Gag p6 consensusepitopes shown in Table 3 below:

TABLE 3 SEQ ID NO Description Sequence 23 Con of ConsSRPEPTAPPA ESFGFGEEIT PSPKQEPKDK ELYPLASLKS LFGNDPLSQ 24 M.group.ancSRPEPTAPPA ESFGFGEEIT PSPKQEPKDK ELYPLASLKS LFGSDPLSQ 25 consensus A1SRPEPTAPPA EIFGMGEEIT SPPKQEQKDR EQDPPLVSLK SLFGNDPLSQ 26 A1.ancSRPEPTAPPA ENFGMGEEMI SSPKQEQKDR EQYPPLVSLK SLFGNDPLSQ 27 consensus A2SRTEPTAPPA ENLRMGEEIT SSLKQELKTR EPYNPAISLK SLFGNDPLSQ 28 consensus BSRPEPTAPPE ESFRFGEETT TPSQKQEPID KELYPLASLR SLFGNDPSSQ 29 B.ancSRPEPTAPPE ESFRFGEETT TPSQKQEPID KELYPLASLK SLFGNDPSSQ 30 consensus CNRPEPTAPPA ESFRFEETTP APKQEPKDRE PLTSLKSLFG SDPLSQ 31 C.ancSRPEPTAPPA ESFRFEETTP APKQEPKDRE PLTSLKSLFG SDPLSQ 32 consensus DSRPEPTAPPA ESFGFGEEIT PSQKQEQKDK ELYPLTSLKS LFGNDPLSQ 33 consensus F1SRPEPTAPPA ESFGFREEIT PSPKQEQKDE GLYPPLASLK SLFGNDP 34 consensus GNRPEPTAPPA ESFGFGEEIA PSPKQEQKEK ELYPLASLKS LFGSDP 35 consensus HSRPEPTAPPA ESFGFGEEMT PSPKQELKDK EPPLASLRSL FGNDPLSQ 36 consensus KSRPEPTAPPA ESFGFGEEIT PSPRQETKDK EQGPPLTSLK SLFGNDPLSQ 37consensus_01_AE SRPEPTAPPA ENWGMGEEIT SLPKQEQKDK EHPPPLVSLK SLFGNDPLSQ38 consensus_02_AG SRPEPTAPPA ESFGMGEEIT SSPKQEPRDK GLYPPLTSLK SLFGNDP39 consensus_03_ABSRPEPSAPPA ENFGMGEEIT PSLKQEQKDR EQHPPSISLK SLFGNDPLSQ 40consensus_04_CP SRPEPTAPPA ESLEMKEETT SSPKQEPRDK ELYPLTSLKS LFGSDPLSQ X41 consensus_06_CP NRPEPTAPPA ESFGFGEETA PSPKQEPKEK ELYPLASLKS LFGNDP X42 consensus_07_BCSRPEPTAPPE ESFRFGEETT TPSQKQEPID KELYPLTSLK SLFGNDPSSQ 43consensus_08_BC SRPEPTAPPA ESFRFEETTP APKQEPKDRE PLTSLRSLFG SDPLSQ 44consensus_10_CD SRPEPTAPPA ESFGFGEEIT PSQKQEQKDK ELHPLASLKS LFGNDPLSQ 45consensus_11_CP SRPEPTAPPA ESFGFGEEIA PSPKQEPKEK ELYPLTSLKS LFGSDPLSQ X46 consensus_12_BF NRPEPTAPPA ESFGFGEEIT PSPKQEQKDE GLYPPLASLK SLFGNDP47 consensus_14_BG NRPEPTAPPA ESFGFGEEIA PSPKQEPKEK EIYPLASLKS LFGSDP$SQ

A blast search of SEQ ID NO:1 failed to identify any identical genesequences. A blast search of SEQ ID NO:2 identified three sequences thatwere 100% identical to SEQ ID NO:2 (Sequence AAC28445 (Fang, H. et al.,(1995) J. Virol. 69(1):75-81; Sequence P12493 (Buckler, C. E. et al.Direct Submission); Sequence AAB04036 (Willey, R. L. et al. (1986) Proc.Natl. Acad. Sci. U.S.A. 83 (14), 5038-5042).

U.S. Pat. No. 6,458,527 relates to an immunoassay to detect the presenceof a human immunodeficiency virus using a GAG antigen that comprises atleast seven contiguous amino acids from a GAG open reading frame thatincludes SEQ ID NO:48:

SRPEPTAPPE ESFRFGEEKT TTPSQKQEPI DKELYPLT S LRSLFGNDPS SN2149       2179       2209       2239       2269       2299

A comparison of this sequence to SEQ ID NO:1 and SEQ ID NO:2 indicatesthat these sequences share more than seven contiguous residues with SEQID NO:48) (Table 4):

TABLE 4 SEQ ID NO Description Sequence 48 GAGSRPEPTAPPEESFRFGEEKTTTPSQKQEPIDKELYPLT•SLRSLFGNDPSSN  1 Isolated EpitopeSRPEPTAPPAESFRFGEEITPTPSQKQEPKDKELYPPLASLRSLFGNDPSSN  2 Isolated EpitopeSRPEPTAPPEESFRFGEET••TPSQKQEPIDKELYPL•ASLRSLFGSDPSSQEF

The identified Gag epitope sequences (SEQ ID NO:1 or SEQ ID NO:2), orany of SEQ ID NOS:3-47 are useful as diagnostic agents in accordancewith the principles of the present invention. SEQ ID NOs:1-7 arepreferred as a gag epitope sequences, and SEQ ID NO:3 is particularlypreferred as a gag epitope sequence.

Identified gp41 Epitopes

HIV-1 Env-gp41 (SEQ ID NO: 49):LIAARTVELL GHSSLKGLRL GWEGLRYLWN LLLYWGRELK ISAINLVDTI AIAVAGWTDR1        10         20         30         40         50         60VIEIGQRIGR AILHIPRRIR QGLERALL          70         80       88CON-ENV-2-gp41 (SEQ ID NO: 50):LIAARIVELL GHSSLKGLRR GWEALKYLWN LLQYWGQELK NSAISL1        10         20         30         40     46ENV-gp41 (SEQ ID NO: 51): LIVTRIVELL GRRGWEALKY WWNLLNYWSQ ELKNSAVNL1        10         20         30        39 Env2-gp41-A-Q(SEQ ID NO: 52) ARIVELLGHS SLKGLRRGWE ALKYLWNLLQ YWGQ1        10         20         30   34 Env3-gp41-seq (SEQ ID NO: 53)CRAILNIPRR IRQGLERALL 1        10         20 Env4-gp41 seq(SEQ ID NO: 54) AVAEGTDRVI EVVQRV 1        10     16 Env34-gp41 seq(SEQ ID NO: 55) AVAEGTDRVI EVVQRVCRAI LNIPRRIRQG FERALL1        10         20         30     36

The identified gp41 epitopes (SEQ ID NO:50 and SEQ ID NO:51) differ insequence from the sequences of previously identified gp41 peptides.Aligning SEQ ID NO:50 and SEQ ID NO:51 against the HIV-1 gp41 sequence(SEQ ID NO:56; NC_(—)001802) yields the following comparison (sites ofSEQ ID NO:56 that are not conserved are shown in single-underline (ifconserved in either SEQ ID NO:50 or SEQ ID NO:51) or in double-underline(if not conserved in either SEQ ID NO:50 or SEQ ID NO:51)) (Table 5):

TABLE 5 SEQ ID NO Description Sequence 50 Isolated EpitopeLIAARIVELLGHSSLKGLRRGWEALKYLWNLLQYWGQELKNSAISL 51 Isolated EpitopeLIVTRIVELLG•••••••RRGWEALKYWWNLLQYWSQELKNSAVNL 56 Gp41LIVTRIVELLG•••••••RRGWEALKYWWNLLQYWSQELKNSAVSL

Thus, both SEQ ID NO:50 and SEQ ID NO:51 differ in sequence from thesequence of the corresponding native HIV-1 gp41 gene product (SEQ IDNO:56). An alignment of these sequences with a series of gp41 consensussequences (Table 6) indicates that SEQ ID NO:50 and SEQ ID NO:51 differin sequence from the consensus sequences.

TABLE 6 SEQ ID NO Description Sequence 56 GP41LIVTRIVELLG•••••••RRGWEALKYWWNLLQYWSQELKNSAVSL 50 Isolated EpitopeLIAARIVELLGHSSLKGLRRGWEALKYLWNLLQYWGQELKNSAISL 51 Isolated EpitopeLIVTRIVELLG•••••••RRGWEALKYWWNLLQYWSQELKNSAVNL 57 Consensus_B (128)LIVTRIVELLG•••••••RRGWEALKYWWNLLQYWSQELKNSAVNL 58 Consensus_D (17)LIAARIVELLG•••••••RRGWEALKYLWNLLQYWIQELKNSAISL 59 Consensus_F1-F2 (10)LIAARTVDRGL•••••••KRGWEALKYLWNLTQYWGQELKNSAISL 60 Consensus_H (3)LIVVRTVELLG•••••••RRGREALKYLWNLLQYWGQELKNSAINL 61 Consensus_A-A1-A2 (24)LIAARTVELLGHSSLKGLRLGWEGLKYLWNLLLYWGRELKISAINL 62 Consensus_C (50)LIAARAVELLGRSSLRGLQRGWEALKYLGSLVQYWGLELKKSAISL 63 Consensus_G (9)LIAARTVELLGRSSLKGLRLGWEGLKYLWNLLLYWGQELKNSAINL 64 Consensus_01 (32)LIAARTVELLGHSSLKGLRRGWEGLKYLGNLLLYWGQELKISAISL 65 Consensus_02 (16)LIAARTVELLGHSSLKGLRLGWEALKYLGNLLSYWGQELKNSAINL

A blast search of SEQ ID NO:50 failed to identify any identical genesequences. A blast search of SEQ ID NO:51 identified two sequences thatwere 100% identical to SEQ ID NO:51 (Sequence AAC28452 (Fang, H. et al.(1995) J. Virol. 69 (1), 75-81; Sequence PO4582 (Ratner, L. et al.(1985) Nature 313:277-284 (1985). Of the sequences that differed fromSEQ ID NO:51 by one amino acid residue, a substitution of L38→N38 wascommon (see, e.g., Sequence CAD10927 (Zheng, N. N. et al., DirectSubmission). SEQ ID NOs:50, 53 and 55 are particularly preferred as gp41epitope sequences.

The invention also relates to the following HIV 1 gp41 consensusepitopes shown in Table 7 below:

TABLE 7 SEQ ID No. Description Sequence 66 CON_OF_CONSLIAARTVELLGRRGWEALKYLWNLLQYWGQELKNSAISLLDTTAIAVAEGTDRVIEVVQRVCRAILNIPRRIRQGFERALL 67 Mgroup.ancLIAARTVELLGRRGWEALKYLWNLLQYWGQELKNSAISLLDTTAIAVAEGTDRVIEVVQRACRAILHIPRRIRQGFERALL 68 CONSENSUS_A1LIAARTVELLGHSSLEGLRLGWEGLKYLWNLLLYWGRELKISAINLVDTIAIAVAGW TDRVIEIGQRIGRAILHIPRRIRQGLERALL 69 A1.ancLIAARTVELLGRSSLEGLRLGWEGLKYLWNLLLYWGRELKISAINLIDTIAIAVAGWTDRVIEIGQRICRAILNIPRRIRQGLERALL 70 CONSENSUS_A2LIAARTVELLGHSSLKGLRLGWEGLKYLWNLLLYWGRELKNSAISLLDTIAVAVAEWTDRVIEIGQRACRAILNIPRRIRQGFERALL 71 CONSENSUS_BLIVTRIVELLGRRGWEVLKYWWNLLQYWSQELKNSAVSLLNATAIAVAEGTDRVIEVVQRACRAILHIPRRIRQGLERALL 72 B.ancLIVARIVELLGRRGWEALKYWWNLLQYWSQELKNSAVSLLNATAIAVAEGTDRVIEVVQRACRAILHIPRRIRQGLERALL 73 CONSENSUS_CLIAARAVELLGRSSLRGLQRGWEALKYLGSLVQYWGLELERSAISLLDTIAIAVAEGTDRIIELIQRICRAIRNIPRRIRQGFEAALQ 74 C.ancLIAARAVELLGRSSLRGLQRGWEALKYLGSLVQYWGLELKKSAISLLDTIAIAVAEGTDRIIELIQRICRAIRNIPRRIRQGFEAALL 75 CONSENSUS_DLIAARIVELLGRRGWEALKYLWNLLQWYIQELKNSAISLFDTTAIAVAEGTDRVIEIVQRACRAILNIPTRIRQGLERALL 76 CONSENSUS_F1LIAARIVDRGLRRGWEALKYLGNLTQYWSQELKNSAISLLNTTAIVVAEGTDRVIEALQRAGRAVLNIPRRIRQGLERALL 77 CONSENSUS_F2LIAARTVDMGLKRGWEALKYLWNLPQYWGQELKNSAISLLDTTAIAVAEGTDRIIEVLQRAGRAVLHIPRRIRQGFERALL 78 CONSENSUS_GLIAARTVELLGRSSLKGLRLGWEGLKYLWNLLLYWGQELKNSAINLLDTIAIAVANWTDRVIEVAQRACRAILNIPRRIRQGLERALL 79 CONSENSUS_HLIVVRTVELLGRRGREALKYLWNLLQYWGQELKNSAINLLNTTAIAVAEGTDRIIEIVQRAWRAILHIPRRIRQGFERTLL 80 CONSENSUS_01_AELIAARTVELLGHSSLKGLRRGWEGLKYLGNLLLYWGQELKISAISLLDATAIAVAGWTDRVIEVAQGAWRAILHIPRRIRQGLERALL 81 CONSENSUS_02_AGLIAARTVELLGHSSLKGLRLGWEALKYLGNLLSYWGQELKNSAINLLDTIAIAVANWTDRVIEIGQRAGRAILNIPRRIRQGLERALL 82 CONSENSUS_03_ABLIAARIVELLGRRGWEALKYWWNLLQYWIQELKSSAINLIDTIAIAVAGWTDRVIEIGQRFCRAIRNIPRRIRQGAEKALQ 83 CONSENSUS_04_CPXLIVARTVELLGIRGWEALKYLWNLLLYWGQELRNSAINLLDTTAIAVAEGTDRIIEAVQRACRAIRNIPRRIRQGLERALL 84 CONSENSUS_06_CPXLIAARTVETLGHRGWEILKYLGNLVCYWGQELKNSAISLLDTTAIAVANWTDRVIEVVQRVFRAFLNIPRRIRQGFERALL 85 CONSENSUS_08_BCLTARGVELLGRNSLRGLQRGWEALKYLGSLVQYWGLELKKSTISLVDTIAIAVAEGTDRIINIVQGICRAIHNIPRRIRQGFEAALQ 86 CONSENSUS_10_CDLIATRIVELLGRRGWEAIKYLWNLLQYWIQELKNSAISLLDTTAIAVAEGTDRAIEIVQRAVRAVLNIPTRIRQGLERALL 87 CONSENSUS_11_CPXLIAARIVETLGRRGWEILKYLGNLAQYWGQELKNSAISLLNATAIAVAEGTDRIIEVVHRVLRAILHIPRRIRQGFERALL 88 CONSENSUS_12_BFLIVTRIVELLGRRGWEVLKYWWNLLQYWSQELKNSAISLLNTTAIVVAEGTDRVIEALQRVGRAILNIPRRIRQGLERALL 89 CONSENSUS_14_BGLIAARTVELLGRSSLKGLRLGWEGLKYLWNLLLYWGRELKNSAINLLDTVAIAVANWTDRAIEVVQRVGRAVLNIPVRIRQGLERALL

The identified HIV-1 gp41 epitope sequences (SEQ ID NO:50 or SEQ IDNO:55), or any of SEQ ID NOS:49-89 are useful as diagnostic agents inaccordance with the principles of the present invention.

As one embodiment of the invention, diagnostic assays are contemplatedwherein an HIV-1 epitope sets are employed wherein the peptide epitopesets consist essentially of HIV-1 gp41 terminal region epitopes or HIV-1GAG p6 epitopes or a combination of gp41 and GAG p6 epitopes. As usedherein, “HIV-1 gp41 terminal region epitopes” refers to epitopescontained on amino acids 784-871 of Consensus aligned seq in Los Alamosdatabase, or mutants or derivatives thereof. As used herein HIV-1 GAG-p6epitopes refers to to epitopes on amino acids 452-502 of Consensusaligned sequence in Los Alamos database, or mutants or derivativesthereof. As used herein, an epitope set will consist essentially of gp41and GAG p6 epitopes when the peptide epitope set does not contain otherepitopes that show significant reactivity (i.e. preferably less than130% of background level, more preferably less than 120% of backgroundlevel, and most preferably less than 110% of background level) withanti-HIV 1 antibodies.

Identified Nef Epitope

NEF Peptide (SEQ ID NO: 90): GLIHSQRRQD ILDLWIYHTQ GYFPDWQNYT PGPGVRYPL1        10         20         30        39

The identified Nef epitope (SEQ ID NO:90) is identical in sequence withthe HIV-1 Nef sequence (NC_(—)001802) (SEQ ID NO:91). An alignment ofthese sequences with a series of Nef consensus sequences (Table 8)indicates that SEQ ID NO:90 is highly conserved.

TABLE 8 SEQ ID NO Description Sequence  91 nefGLIHSQRRQDILDLWIYHTQGYFPDWQNYTPGPGVRYPL  90 Isolated EpitopeGLIHSQRRQDILDLWIYHTQGYFPDWQNYTPGPGVRYPL  92 Consensus_B (266)GLIYSQKRQDILDLWVYHTQGYFPDWQNYTPGPGIRYPL  93 Consensus_D (4)GLIWSQKRQEILDLWVYHTQGFFPDWQNYTPGPGIRYPL  94 Consensus_A-A1-A2 (14)GLIYSKKRQEILDLWVYHTQGYFPDWQNYTPGPGIRYPL  95 Consensus_C (44)GLIYSKKRQEILDLWVYHTQGYFPDWQNYTPGPGVRYPL  96 Consensus_F1-F2 (7)GLIYSKKRQDILDLWVYHTQGYFPDWQNYTPGPGIRYPL  97 Consensus_01 (31)GLIYSKKRQEILDLWVYNTQGFFPDWQNYTPGPGIRYPL  98 Consensus_02 (12)GLIYSKKRQEILDLWVYHTQGFFPDWQNYTPGPGTRFPL  99 Consensus_G (7)GLIYSKKRQEILDLWVYNTQGFFPDWQNYTPGPGTRFPL 100 Consensus_H (5)GLIYSKKRQEILDLWVYNTQGYFPDWQNYTPGPGERYPL

The identified nef epitope sequence (SEQ ID NO:90), or any of SEQ IDNOS:92-100 are useful as diagnostic agents in accordance with theprinciples of the present invention.

Identified HIV-2 Epitopes

As one aspect of the invention, it is contemplated that peptidescomprising epitopes that are contained on HIV-2 Env-gp36 (e.g. aminoacids 817-927 of MAC.US.-0.239_M33262 ENV aligned seq in Los Alamosdatabase, or mutants or derivatives thereof) or epitopes that arecontained on HIV-2 GAG-p6 (amino acids 461-555 of MAC.US.-0.239_M33262GAGPRO aligned seq in Los Alamos database, or mutants or derivativesthereof) will be useful in the diagnosis of HIV-2 infection. Inparticular, it is contemplated as an aspect of the invention that acombination of at least one epitope contained on HIV-2 gp36 and at leastone epitope contained on HIV-2 GAG-p6 will be useful in the diagnosis ofbreakthrough HIV-2 infections in individuals that have been vaccinatedagainst the HIV-1 or HIV-2 virus, or viral genes or gene products ofthese viruses.

HIV-2 GAG-p6 (SEQ ID NO: 101)APQGLIPTAP PMNPAFGMTP QGAIPSAPPA DPAADLLEKY LQQGRKQREQ RERPYKEVTE1        10         20         30         40         50         60DLLHLEQGET PRREATEDLL HLNSLFGKDQ          70         80         90HIV-2 Env-gp36 (SEQ ID NO: 102)FLIRLLIRLL IGLYNICRTL ISKSFQTLQP ISQGLQRALT AIRDWLRPGA AYLQYGCEWI1        10         20         30         40         50         60QEALQAFARA TRETLTSVWR NFCGTMGQIG RGILAIPRRI RQGAELALL         70         80         90         100       109

The invention also relates to HIV-2 GAG p6 and HIV-2 Env-gp36 epitopesshown below in Table 9 and Table 10, respectively.

TABLE 9 SEQ ID NO Description Sequence 103 MAC.US.-.239VHQGLMPTAPPEDPAVDLLKNYMQLGKQQREKQRESREKPYKEVTEDLLHLN _M33262 SLFGGDQ 104H2A.CI.88.UC2 APQGLIPTAPPADPAADLLEKYLQQGRKQREQRERPYKEVTEDLLHLEQGET_U38293 PRRE-ATEDLLHLNSLFGKDQ 105 MAC.US.-.MM142VHQGLTPTAPPEEPAVDLLKNYMHLGKQQRESRGKPYKEVTEDLLHLNSLFG _M16403 GDQ 106MNE.US.-.MNE027 MEQGLTPTAPPEDPAVDLLKNYMQLGKQQRESKRKPYKEVAEDLLELNSLFG_U79412 EDQ 107 SMM.US.-.H9MPQGLTPTAPPEDPAVDLLKNYMKVGRRQRENRERPYKEVTEDLLHLNSLFG _M80194 EDQ 108H2B.CI.-.EHO APQGIVPSAPPMNPAFGMTPQGAIPSAPPADPAEEMLKNYMQLGKKQKENRE_U27200 RPYKEVTEDLLHLNSLFGEDQ 109 H2B.CI.88.UC1VPQGVTPSAPPMDPAEGMTPRGATPSAPPADPAVEMLKSYMRMGRQQRESRE _L07625RPYKEVTEDLLHLNSLFGEDQ 110 H2B.GH.86.D205VPQGVTPSAPPMNPAEGMTPRGATPSAPPADPAVEMLKSYMQMGRQQRESRE _X61240RPYKEVTEDLLHLNSLFGEDQ 111 H2B.JP.01.KR020APQGILPSAPPMNPAENMTPQGAMPSAPPADPAVEMLKDYMQLGRKQKGGRE _AB100245KPYKEVTEDLLHLNSLFGEDQ 112 H2G.CI-.ABT96VPQGLTPSAPPMDPAVDLLKNYMQLGRKQKEQRNKPYKEVTEXLLHLSSLFG _AF208027 DDQ 113H2U.FR.96.12034 VPQGLTPTAPPAEPAVDLLTPTAPPADPAVDLLKSYMQQGKKQKENRERPYK_AY530889 EVTEDLLHLNSLFGNDQ 114 H2AB.CI.-.7312AVPQEIVPSAPPMNTAEGKTHQGAIPSAPPADPAVEMLKSYMQLGKQQREKQG _L36874RPYKEVTEDLLHLNSLFGEDQ 115 SMM.SL.92.SL92BTTSLTPSAPPDPAARIVKEYLEKAQREKTRRSRPYKEVTEDLLHLNSLFGED _AF334679 Q

TABLE 10 SEQ ID NO Description Sequence 116 MAC.US.-FLIRQLIRLLTWLFSNCRTLLSRVYQILQPILQRLSATLQRIREVLRTELTYLQYGW .239_M33262SYFHEAVQAVWRSATETLAGAWGDLWETLRRGGRWILAIPRRIRQGLELTLL 117 H2A.-.-FLIRLLIRLLIGLYNICRTLISKSFQTLQPISQGLQRALTAIRDWLRPGAAYLQYGC .CBL21_U0535EWIQEALQAFARATRETLTSVWRNFCGTMGQIGRGILAIPRRIRQGAELALL 0 118 H2A.CI.88.UC2LLIHLLTRLLTGLYSICRDLLSANSPTRRLISQNLTAIRDWLRLKAAYLQYGCEWIQ _U38293EAFQAIARTARETLAGAWRGLCKAVQRIGRGILAVPRRIRQGAEIALL 119 H2A.DE.-FLIHLLTRLLIGLYNICRDLLSKNSPTRRLISQSLTAIRDWLRLKAAQLQYGCEWIQ .BEN_M30502EAFQAFARTTRETLAGAWGWLWEAARRIGRGILAVPRRIRQGAELALL 120 H2A.GH.-FLIHLLTRLLTGLYKICRDLLSTNSPTHRLISQNLTAIRDWLRLKAAYLQYGGEWIQ .GH1_M30895EAFQAFAKTTRETLASAWGGLCAAVQRVGRGILAVPRRIRQGAEIALL 121 H2A.GM.87.D1FLIHLLTRLLTGLYNSCRGLLSKNSPTRRLISQSLTAIRDWLRLKAAYLQYGCEWIQ 94_J04542EAFRAFARTARETIAGAWRGLCEAAQRIGRGILAVPRRIRQGAEIALL 122 H2A.GM.90.CBFLIRLLIRLLIGLYNICRDLLSRSSLILQPILQSLQRALTAIRDWLRLEAAYLQYGC L24_U05353EWIQEALQALTRATRETLAGAWRNLWGALQRIGRGILAVPRRIRQGAELALL 123 H2A.GW.-FLIRLLIRLLTRLYNSCRDLLSRSFLTLQPIFQNLRDWLRLRTAFLQYGRQWIQEAF .CAM3_U05355QAFARATRETLTSACRGLWRTLDNFGRGILSIPRRIRQGAEIALL 124 H2A.SN.-FLIRQLIRLLNRLYNICRDLLSRSFQTLQLISQSLRRALTAVRDWLRFNTAYLQYGG .ST_M31113EWIQEAFRAFARATGETLTNAWRGFWGTLGQIGRGILAVPRRIRQGAEIALL 125 H2A.SN.85.ROFLIRQLIRLLTRLYSICRDLLSRSFLTLQLIYQNLRDWLRLRTAFLQYGCEWIQEAF D_M15390QAAARATRETLAGACRGLWRVLERIGRGILAVPRRIRQGAEIALL 126 H2A.GM.-FLIRLLIRLLTRLYNSCRDLLSRLYLILQPLRDWLRLKAAYLQYGCEWIQEAFQALA .ISY_J04498RVTRETLTSAGRSLWGALGRIGRGILAVPRRIRQGAEIALL 127 H2B.CI.-FPIRQLRDLLIWLYSGCRTLLSKTFQTLQPVLQPLRLPPAYLRYGISWFQEAIQAAA .EHO_U27200RAAGETLASAARTSWGVLRRAAGEIIAIPRRIRQGAELALL 128 H2B.GH.86.D2FLLRQLRNLLIWLYNGCRTLLLKTFQILHQISTNLQPLRLPVAYLQYGISWFQEALR 05_X16109AAARATGETLASAGETLWEALRRAARAIIAIPRRIRQGLELTLL 129 H2G.CI.-ABTFLXRQLGNLLTWLYSNCRALLSRIXQTLQPLFQRISRTLQAIREHLRLEAAYFSYGF 96_AF208027RWLQEACTAATRAAQETLTSTWRALWKTLGRVGRGILAIPRRIRQGLELTLL 130 H2U.FR.96.120FLIHQLIRLLTWLYSSCRDLLSRICQSLQPLFQSIRERLHLEIAYLQYGWQYFKEAF 34_AY530889QAFGKAARETLSRTGRELWETLGRVGRWLRAIPRRIRQGFELALL 131 H2AB.CI.-FLIRQLRNLLIWLYDGCRTLLLKTFQTLQPALQPLRLLFAYLQYGIGWFQEAVQAAA .7312A_L36874GATGETLASTGRTLWEALRRTARGIIAVPRRIRQGLELALL 132 MAC.US.-FLIRQLIRLLTWLFSNCRTLLSRVYQILQPIFQRLSATLQRIREVLRTELTYLQYGW .BR5_AY29071SYFHEAVQAVWRSATETLAGAWGDLWETLARGGRW 6 133 MAC.US.-.BRFLIRQLIRLLTWLFSNCRTLLSRVYQILQPMFQGLSATLQRIREVLRTELTYLQYGW 5_AY290710SYFHEAVQAVWRAATETLAGAWGDLWETLRRGGRW 134 MAC.US.-.BRFLIRQLIRLLTWLFSNCRTLLSRVYQILQPIFQGLSATLQRIREVLATELTYLQYGW 5_AY290709SYFHEAVQAVWRAATETLAGAWGDLWETLRRGGRW 135 MNE.US.-.MNFLIRQLIRLLTWLFSNCRTLLSRAYQILQPIFQRFSTTLQRVREVLRTELTYLQYGW E027_U79412SYFQEAVQVAWRSATETLAGAWGDLWETLGRVGRWILAIPRRIRQELELTLL 136 SMM.SL.92.SLFLIRQLIRILTWLYNNLTRLASRAYQNLQQLCQRLSEISQPIRELVRREAGYIRYGW 92B_AF334679NYFIEACQEAWRSAQEAIVGAWGLIWETLGRVGRGIAAIPRRIRQGLELMLN 137 SMM.US.-.PTFLIRQLIRLLTWLFSSCRDWLLRIYQILQPVLQGLSRTLQRVREVIRIEITYLQYGW 583_AY221512SYFQEAAQAWWKFARETLASAWRDIWETLGRVGRGILAIPRRVRQGLELALL

The identified HIV-2 GAG-p6 epitope sequence (SEQ ID NO:101), or any ofSEQ ID NOS:103-115 are useful as diagnostic agents in accordance withthe principles of the present invention. Likewise, the identified HIV-2Env-gp36 epitope sequence (SEQ ID NO:102), or any of SEQ ID NOS:116-137are useful as diagnostic agents in accordance with the principles of thepresent invention.

As one embodiment of the invention, diagnostic assays are contemplatedwherein HIV-2 epitope sets are employed, wherein the epitope setsconsist essentially of HIV-2 GAG-p6 epitopes or HIV-2 Env-gp36 epitopes.As used herein, an epitope set will consist essentially of HIV-2 GAG-p6epitopes and HIV-2 Env-gp36 epitopes when the peptide epitope set doesnot contain other epitopes that show significant reactivity (i.e.preferably less than 130% of background level, more preferably less than120% of background level, and most preferably less than 110% ofbackground level) with anti-HIV 2 antibodies.

Peptide molecules containing the epitopes of the invention may beprepared using virtually any art-known technique for the preparation ofpeptides. For example, the peptides may be prepared using conventionalstep-wise solution or solid phase peptide syntheses, or recombinant DNAtechniques or proteolysis or modifications of purified viralproteins/peptides or recombinant proteins. Peptides may be preparedusing conventional step-wise solution or solid phase synthesis (see,e.g., Merrifield, R B. (1969) “SOLID-PHASE PEPTIDE SYNTHESIS,” Adv.Enzymol. Relat Areas Mol. Biol. 32:221-296; Fairwell, T. et al. (1987)“HUMAN PLASMA APOLIPOPROTEIN C-II: TOTAL SOLID-PHASE SYNTHESIS ANDCHEMICAL AND BIOLOGICAL CHARACTERIZATION,” Proc. Natl. Acad. Sci. U.S.A84:4796-4800; Kent, S. B. H. “CHEMICAL SYNTHESIS OF PEPTIDES ANDPROTEINS,” (1988) Ann. Rev. Biochem. 57, 957-984, CHEMICAL APPROACHES TOTHE S YNTHESIS OF PEPTIDES AND PROTEINS, Williams et al., Eds., 1997,CRC Press, Boca Raton Fla., and references cited therein; SOLID PHASEPEPTIDE SYNTHESIS: A PRACTICAL APPROACH, Atherton & Sheppard, Eds.,1989, IRL Press, Oxford, England, and references cited therein).

Alternatively, such peptides of the invention may be prepared by way ofsegment condensation, as described, for example, in Schnölzer, M. etal., “CONSTRUCTING PROTEINS BY DOVETAILING UNPROTECTED SYNTHETICPEPTIDES: BACKBONE-ENGINEERED HIV PROTEASE,” Science. 1992 Apr. 10;256(5054):221-5; Schnölzer, M., “IN SITU NEUTRALIZATION IN BOC-CHEMISTRYSOLID PHASE PEPTIDE SYNTHESIS. RAPID, HIGH YIELD ASSEMBLY OF DIFFICULTSEQUENCES ,” Int Pept Protein Res. 1992 September-October; 40(3-4):180-193; Rose et al., “STEPWISE SOLID-PHASE SYNTHESIS OFPOLYAMIDES AS LINKERS,” J. Am. Chem. Soc. 1999 August 4, 121:7034-7038.Methods for preparing peptides are disclosed in U.S. Pat. Nos. 6,004,925and 6,429,289.

Assays for the Detection of HIV-1 and HIV-2

The present invention is directed in part to the use of novel epitopesin diagnostic assays for the detection of HIV-1 or HIV-2. In a preferredembodiment, such assays of HIV will comprise enzyme immunosorbent assays(EIAs) that employ one or more of the above-described gp41, GAG and/ornef peptides, or fragments or variants thereof, or one or more of theabove described HIV-2 GAG or Env-gp36 peptides, or fragments or variantsthereof. In a preferred embodiment, 1, 2 or 3 such peptides are employedin such assays. The selected peptides, alone or in combination, can beused to differentiate between vaccine directed antibodies andbreakthrough infection generated antibodies to assess the efficacy ofvaccine clinical trials, or to monitor potential infections.

Fragments or variants of the peptides preferably comprise at least 10,20 or 30 contiguous amino acids of the peptides and are at least 70%,preferably at least 75%, 80%, or 85%, more preferably at least 90%, andmost preferably at least 95% homologous to the indicated peptides.

A preferred method for determining the best overall match between aquery sequence (a sequence of the present invention) and a subjectsequence (i.e. homology), also referred to as a global sequencealignment, can be determined using the FASTDB computer program based onthe algorithm of Brutlag et al., 1990, Comp. App. Biosci. 6:237-245. Ina sequence alignment the query and subject sequences are both amino acidsequences. The result of said global sequence alignment is in percentidentity. Preferred parameters used in a FASTDB amino acid alignmentare: Matrix=PAM 0, k-tuple=2, Mismatch Penalty=1, Joining Penalty=20,Randomization Group Length=0, Cutoff Score=1, Window Size=sequencelength, Gap Penalty=5, Gap Size Penalty=0.05, Window Size=500 or thelength of the subject amino acid sequence, whichever is shorter.

If the subject sequence is shorter than the query sequence due to N- orC-terminal deletions, not because of internal deletions, a manualcorrection must be made to the results. This is because the FASTDBprogram does not account for N- and C-terminal truncations of thesubject sequence when calculating global percent identity. For subjectsequences truncated at the N- and C-termini, relative to the querysequence, the percent identity is corrected by calculating the number ofresidues of the query sequence that are N- and C-terminal of the subjectsequence, which are not matched/aligned with a corresponding subjectresidue, as a percent of the total residues of the query sequence.Whether a residue is matched/aligned is determined by results of theFASTDB sequence alignment. This percentage is then subtracted from thepercent identity, calculated by the above FASTDB program using thespecified parameters, to arrive at a final percent identity score. Thisfinal percent identity score is what is used for the purposes of thepresent invention. Only residues to the N- and C-termini of the subjectsequence, which are not matched/aligned with the query sequence, areconsidered for the purposes of manually adjusting the percent identityscore. That is, only query residue positions outside the farthest N- andC-terminal residues of the subject sequence.

For example, a 90 amino acid residue subject sequence is aligned with a100 residue query sequence to determine percent identity. The deletionoccurs at the N-terminus of the subject sequence and therefore, theFASTDB alignment does not show a matching/alignment of the first 10residues at the N-terminus. The 10 unpaired residues represent 10% ofthe sequence (number of residues at the N- and C-termini notmatched/total number of residues in the query sequence) so 10% issubtracted from the percent identity score calculated by the FASTDBprogram. If the remaining 90 residues were perfectly matched the finalpercent identity would be 90%. In another example, a 90 residue subjectsequence is compared with a 100 residue query sequence. This time thedeletions are internal deletions so there are no residues at the N- orC-termini of the subject sequence which are not matched/aligned with thequery. In this case the percent identity calculated by FASTDB is notmanually corrected. Once again, only residue positions outside the N-and C-terminal ends of the subject sequence, as displayed in the FASTDBalignment, which are not matched/aligned with the query sequence aremanually corrected for. No other manual corrections are to be made forthe purposes of the present invention.

The present invention concerns the binding of peptide eptitopes andantibodies. As used herein, an “epitope” is a 2- or 3-dimensional regionof an antigen that is recognized by and that specifically binds to anantibody. As used herein, an epitope and an antibody are said to be“specific” for one another, or to “recognize” one another, or to “bind”to one another if they are capable of immunospecific binding to oneanother.

Any of a wide variety of assay formats may be used in accordance withthe methods of the present invention. Such formats may be heterogeneousor homogeneous, sequential or simultaneous, competitive ornoncompetitive. U.S. Pat. Nos. 5,563,036; 5,627,080; 5,633,141;5,679,525; 5,691,147; 5,698,411; 5,747,352; 5,811,526; 5,851,778; and5,976,822 illustrate several different assay formats and applications.Such assays can be formatted to be quantitative, to measure theconcentration or amount of an anti-HIV antibody, or they may beformatted to be qualitative, to measure the presence or absence of ananti-HIV antibody. Additional descriptions of immunoassays that may beadapted for use in accordance with the principles of the presentinvention are available in the scientific literature (Gnann, J. W. Jr etal. “CUSTOM-DESIGNED SYNTHETIC PEPTIDE IMMUNOASSAYS FOR DISTINGUISHINGHIV TYPE 1 AND TYPE 2 INFECTIONS,” Methods Enzymol. 1989; 178:693-714;Dopel, S. H. et al. “COMPARISON OF FOUR ANTI-HIV SCREENING ASSAYS WHICHBELONG TO DIFFERENT TEST GENERATIONS,” Eur J Clin Chem Clin Biochem.1991 May; 29(5):331-7; Manocha, M. et al. “COMPARING MODIFIED AND PLAINPEPTIDE LINKED ENZYME IMMUNOSORBENT ASSAY (ELISA) FOR DETECTION OF HUMANIMMUNODEFICIENCY VIRUS TYPE-1 (HIV-1) AND TYPE-2 (HIV-2) ANTIBODIES,”Immunol Lett. 2003 Feb. 3; 85(3):275-8); Brattegaard, K. et al.“INSENSITIVITY OF A SYNTHETIC PEPTIDE-BASED TEST (PEPTI-LAV 1-2) FOR THEDIAGNOSIS OF HIV INFECTION IN AFRICAN CHILDREN,” AIDS. 1995 June;9(6):656-7; Beristain, C. N. et al. “EVALUATION OF A DIPSTICK METHOD FORTHE DETECTION OF HUMAN IMMUNODEFICIENCY VIRUS INFECTION,” J Clin LabAnal. 1995; 9(6):347-50; Modrow, S. et al. “CARRIER BOUND SYNTHETICOLIGOPEPTIDES IN ELISA TEST SYSTEMS FOR DISTINCTION BETWEEN HIV-1 ANDHIV-2 INFECTION,” J Acquir Immune Defic Syndr. 1989; 2(2):141-8;Gueye-Ndiaye, A. et al. “COST-EFFECTIVE DIAGNOSIS OF HIV-1 AND HIV-2 BYRECOMBINANT-EXPRESSED ENV PEPTIDE (566/996) DOT-BLOT ANALYSIS,” AIDS.1993 April; 7(4):475-81; Sabatier, J. M. et al. “USE OF SYNTHETICPEPTIDES FOR THE DETECTION OF ANTIBODIES AGAINST THE NEF REGULATINGPROTEIN IN SERA OF HIV-INFECTED PATIENTS,” AIDS. 1989 April;3(4):215-20; Sommerfelt, M. A. et al. “NOVEL PEPTIDE-BASED HIV-1IMMUNOTHERAPY,” Expert Opin Biol Ther. 2004 March; 4(3):349-361; Alcaro,M. C. et al. “SYNTHETIC PEPTIDES IN THE DIAGNOSIS OF HIV INFECTION,”Curr Protein Pept Sci. 2003 August; 4(4):285-90; Smith, R. S. et al.“SYNTHETIC PEPTIDE ASSAYS TO DETECT HUMAN IMMUNODEFICIENCY VIRUS TYPES 1AND 2 IN SEROPOSITIVE INDIVIDUALS,” Arch Pathol Lab Med. 1990 March;114(3):254-8; Petrov, R. V. et al. “THE USE OF SYNTHETIC PEPTIDES IN THEDIAGNOSIS OF HIV INFECTIONS,” Biomed Sci. 1990 March; 1(3):239-44;Zolla-Pazner S. “IDENTIFYING EPITOPES OF HIV-1 THAT INDUCE PROTECTIVEANTIBODIES,” Nat Rev Immunol. 2004 March; 4(3):199-210; Baillou, A. etal. “FINE SEROTYPING OF HUMAN IMMUNODEFICIENCY VIRUS SEROTYPE 1 (HIV-1)AND HIV-2 INFECTIONS BY USING SYNTHETIC OLIGOPEPTIDES REPRESENTING ANIMMUNODOMINANT DOMAIN OF HIV-1 AND HIV-2/SIMIAN IMMUNODEFICIENCY VIRUS,”J Clin Microbiol. 1991 July; 29(7):1387-91; McGaughey, G. B. et al.“PROGRESS TOWARDS THE DEVELOPMENT OF A HIV-1 GP41-DIRECTED VACCINE,”Curr HIV Res. 2004 April; 2(2):193-204).

Heterogeneous immunoassay techniques typically involve the use of asolid phase material to which the reaction product becomes bound, butmay be adapted to involve the binding of non-immobilized antigens andantibodies (i.e., a solution-phase immunoassay). The reaction product isseparated from excess sample, assay reagents, and other substances byremoving the solid phase from the reaction mixture (e.g., by washing).One type of solid phase immunoassay that may be used in accordance withthe present invention is a sandwich immunoassay. In the sandwich assay,the more analyte present in the sample, the greater the amount of labelpresent on the solid phase. This type of assay format is generallypreferred, especially for the visualization of low analyteconcentrations, because the appearance of label on the solid phase ismore readily detected.

In accordance with a preferred embodiment of the present invention, apeptide of the present invention that is specifically reactive with ananti-HIV antibody is bound to a solid support (i.e., immobilized) andincubated in contact with the biological sample being tested for thepresence of an anti-HIV antibody. A blocking agent may be added toreduce non-specific binding.

As will be appreciated, the peptide may be incubated with the biologicalsample in an unbound state and then subsequently bound to the solidsupport (i.e., immobilizable). The supports are then preferablyextensively treated (e.g., by washing, etc.) to substantially removenon-HIV antibodies that may be present but that failed to bind to thebound peptide. In consequence of such treatment, an immune complex formsbetween the peptide and anti-HIV antibody.

A detectably labeled second antibody (capable of binding to the initialantibody (e.g., an anti-human IgG antibody)) is then preferably addedand the support is incubated under conditions sufficient to permit thesecond antibody to bind to any anti-HIV antibody that may be present.The support is then preferably extensively treated (e.g., by washing,etc.) to substantially remove any unbound second antibody. If anti-HIVantibody is present in the test sample, then the two antibodies willform an immune complex with the immobilized peptide (i.e., a secondantibody/anti-HIV antibody/immobilized peptide sandwich). In such anassay, the detection of second antibody bound to the support isindicative of anti-HIV antibody in the sample being tested. Sandwichassay formats are described by Schuurs et al. U.S. Pat. Nos. 3,791,932and 4,016,043, and by Pankratz, et al., U.S. Pat. No. 5,876,935. Thesecond antibody may be a natural immunoglobulin isolated from nonhumanspecies (e.g., anti-human IgG murine antibody, anti-human IgG goatantibody, anti-human IgM goat antibody, etc.), or it can be producedrecombinantly or synthetically. It may be an intact immunoglobulin, oran immunoglobulin fragment (e.g., FAb, F[Ab]₂, etc.). As desired, otherbinding molecules (capable of binding to anti-HIV antibodies) may beemployed in concert with or in lieu of such second antibodies. Forexample, the anti-HIV antibodies can be biotinylated and the secondantibody can be replaced with labeled avidin or streptavidin.

To eliminate the bound-free separation step and reduce the time andequipment needed for a chemical binding assay, a homogeneous assayformat may alternatively be employed. In such assays, one component ofthe binding pair may still be immobilized; however, the presence of thesecond component of the binding pair is detected without a bound-freeseparation. Examples of homogeneous optical methods are the EMIT methodof Syva, Inc. (Sunnyvale, Calif.), which operates through detection offluorescence quenching; the laser nephelometry latex particleagglutination method of Behringwerke (Marburg, Germany), which operatesby detecting changes in light scatter; the LPIA latex particleagglutination method of Mitsubishi Chemical Industries (Tokyo, Japan);the TDX fluorescence depolarization method of Abbott Laboratories(Abbott Park, Ill.); and the fluorescence energy transfer method of CisBio International (Paris, France). Any of such assays may be adapted foruse in accordance with the objectives of the present invention.

The binding assay of the present invention may be configured as acompetitive assay. In a competitive assay, the more anti-HIV antibodypresent in the test sample, the lower the amount of label present on thesolid phase.

In a manner similar to the sandwich assay, the competitive assay can beconducted by providing a defined amount of a labeled anti-HIV antibodyand determining whether the fluid being tested contains anti-HIVantibody that would compete with the labeled antibody for binding to thesupport. In such a competitive assay, the amount of captured labeledantibody is inversely proportional to the amount of analyte present inthe test sample. Smith (U.S. Pat. No. 4,401,764) describes analternative competitive assay format using a mixed binding complex thatcan bind analyte or labeled analyte but in which the analyte and labeledanalyte cannot simultaneously bind the complex. Clagett (U.S. Pat. No.4,746,631) describes an immunoassay method using a reaction chamber inwhich an analyte/ligand/marker conjugate is displaced from the reactionsurface in the presence of test sample analyte and in which thedisplaced analyte/ligand/marker conjugate is immobilized at a secondreaction site. The conjugate includes biotin, bovine serum albumin, andsynthetic peptides as the ligand component of the conjugate, andenzymes, chemiluminescent materials, enzyme inhibitors, andradionucleotides as the marker component of the conjugate. Li (U.S. Pat.No. 4,661,444) describes a competitive immunoassay using a conjugate ofan anti-idiotype antibody and a second antibody, specific for adetectable label, in which the detectable response is inversely relatedto the presence of analyte in the sample. Allen (European Patent Appln.No. 177,191) describes a binding assay involving a conjugate of a ligandanalog and a second reagent, such as fluorescein, in which the conjugatecompetes with the analyte (ligand) in binding to a labeled bindingpartner specific for the ligand, and in which the resultant labeledconjugate is then separated from the reaction mixture by means of solidphase carrying a binding partner for the second reagent. This bindingassay format combines the use of a competitive binding technique and areverse sandwich assay configuration; i.e., the binding of conjugate tothe labeled binding member prior to separating conjugate from themixture by the binding of the conjugate to the solid phase. The assayresult, however, is determined as in a conventional competitive assay inwhich the amount of label bound to the solid phase is inverselyproportional to the amount of analyte in the test sample. Chieregatt etal. (GB Patent No. 2,084,317) describe a similar assay format using anindirectly labeled binding partner specific for the analyte. Mochida etal. (U.S. Pat. No. 4,185,084) also describe the use of a double-antigenconjugate that competes with an antigen analyte for binding to animmobilized antibody and that is then labeled. This method also resultsin the detection of label on a solid phase in which the amount of labelis inversely proportional to the amount of analyte in the test sample.Sadeh et al. (U.S. Pat. No. 4,243,749) describe a similar enzymeimmunoassay in which a hapten conjugate competes with analyte forbinding to an antibody immobilized on a solid phase. Any of such variantassays may be used in accordance with the present invention.

In all such assay formats, at least one component of the assay reagentswill preferably be labeled or otherwise detectable by the evolution orquenching of light. Such component may be a second antibody, anti-HIVantibody, or the peptide that binds to the anti-HIV antibody, dependingon the immunoassay format employed. Radioisotopic-binding assay formats(e.g., a radioimmunoassay, etc.) employ a radioisotope as such label;the signal is detectable by the evolution of light in the presence of afluorescent or fluorogenic moiety (see Lucas et al., U.S. Pat. No.5,698,411 and Landrum et al., U.S. Pat. No. 5,976,822).Enzymatic-binding assay formats (e.g., an ELISA, etc.) employ an enzymeas a label; the signal is detectable by the evolution of color or lightin the presence of a chromogenic or fluorogenic moiety. Other labels,such as paramagnetic labels, materials used as colored particles, latexparticles, colloidal metals such as selenium and gold, and dye particles(see U.S. Pat. Nos. 4,313,734; 4,373,932, and 5,501,985) may also beemployed. The use of enzymes (especially alkaline phosphatase,β-galactosidase, horse radish peroxidase, or urease) as the detectablelabel (i.e., an enzyme immunoassay or EIA) is preferred.

The presence of enzymatic labels may be detected through the use ofchromogenic substrates (including those that evolve or adsorbfluorescent, UV, visible light, etc.) in response to catalysis by theenzyme label. More preferably, chemical labels may be employed (e.g.,colloidal gold, latex bead labels, etc.). Detection of label can beaccomplished using multiple detectors, multipass filters, gratings, orspectrally distinct fluors (see e.g., U.S. Pat. No. 5,759,781), etc. Itis particularly preferred to employ peroxidase as an enzyme label,especially in concert with the chromogenic substrate 3, 3′,5,5′-tetramethylbenzidine (TMB), OPD, or ABTS. In the case of labeling ofthe antibodies with peroxidase as enzyme, it is possible to use theperiodate technique (Nakane, P. K. et al. (1974) “PEROXIDASE-LABELEDANTIBODY. A NEW METHOD OF CONJUGATION,” J Histochem Cytochem.22:1084-90) or a method reported in which the partners are linked with aheterobifunctional reagent (Ishikawa, E. et al. (1983) “ENZYME-LABELINGOF ANTIBODIES AND THEIR FRAGMENTS FOR ENZYME IMMUNOASSAY ANDIMMUNOHISTOCHEMICAL STAINING,” J. Immunoassay. 49(3):209-327).

Any of a wide variety of solid supports may be employed in theimmunoassays of the present invention. Suitable materials for the solidsupport are synthetics such as polystyrene, polyvinyl chloride,polyamide, or other synthetic polymers, natural polymers such ascellulose, as well as derivatized natural polymers such as celluloseacetate or nitrocellulose, and glass, especially glass fibers. Thesupport can take the form of spheres, rods, tubes, and microassay ormicrotiter plates. Sheet-like structures such as paper strips, smallplates, and membranes are likewise suitable. The surface of the carrierscan be permeable and impermeable for aqueous solutions.

Although the foregoing description pertains to assaying for the presenceof anti-HIV antibodies in biological samples that are fluids (e.g.,sera, blood, urine, saliva, pancreatic juice, cerebrospinal fluid,semen, etc.), it will be appreciated that any fluidic biological sample(e.g., tissue or biopsy extracts, extracts of feces, sputum, etc.) maylikewise be employed in the assays of the present invention. Mostpreferably, the biological sample being assayed will be serum or plasma.Table 11 illustrates the variables that may be employed in an ELISA(BSA—bovine serum albumin; FBS—fetal bovine serum; HRP—horsradishperoxidase; AP—alkaline phosphatase; TMB—3, 3′,5,5′-tetramethylbenzidine; OPD—o-phenylenediamine dihydrochloride).

TABLE 11 Epitope Coating Blocking Serum/Plasma 2^(nd) 2^(nd) AntibodyPresentation Amount Agent Dilution Antibody Dilution Substrate GSTProtein 1,000 ng  BSA 1:50 HRP-Anti-Human 1:1,000 Slow TMB (Sigma) IgGPeptide 500 ng BSA 1:100 HRP-Anti-Human 1:2,000 Turbo TMB (ICN) IgG +IgM Biotin- 400 ng Gelatin HRP-Anti-Human 1:5,000 Ultra TMB PeptideIgG + IgM-Fc 250 ng FBS AP-Anti-Human 1:10,000 OPD IgG + IgM (Pierce)100 ng Milk AP-Anti-Human 1:20,000 OPD (NEN) IgG + IgM-Fc  33 ngHRP-Anti-Human ABTS IgG-Fc

In a preferred embodiment of the present invention, the ELISA employs apeptide for epitope presentation, a 33 ng (for GAG-p6) or 250 ng (forEnv-gp41) coating, blocking by milk, a HRP-Anti-Human IgG+IgG-Fc as the2^(nd) antibody (at a 10,000 fold dilution), and OPD as a substrate.Buffers that may be employed include commonly used buffers such as PBSor Tris buffers, with or without Tween-20 or other detergents commonlyused for immunoassays.

Materials for use in the assay of the invention are ideally suited forthe preparation of a kit. Such a kit may comprise a carrier means beingcompartmentalized to receive in close confinement; one or morecontainers means vials, tubes and the like; each of the containers meanscomprising one of the separate elements to be used in the method. Forexample, one of the containers means may comprise a peptide of thepresent invention (for example, any of SEQ ID NOS: 1-11 or 49-55 or 141,with or without the a peptide linker, e.g. a carboxy-terminal GGGC (SEQID NO:138) peptide linker) bound to a solid support A second containermay comprise soluble, detectably labeled second antibody, preferably inlyophilized form, or in solution. In addition, the kit may also containone or more containers, each of which comprises a (different)predetermined amount of an anti-HIV antibody. These latter containerscan be used to prepare a standard curve into which can be interpolatedthe results obtained from the sample containing the unknown amount ofanti-HIV antibodies.

In using the kit, all the user need do is add to a container apremeasured amount of a sample suspected of containing a measurable yetunknown amount of anti-HIV antibody, a premeasured amount ofsupport-hound peptide present in the first container, and a premeasuredamount of the detectably labeled second antibody present in the secondcontainer. After an appropriate time for incubation, an immune complexis formed (if the sample contained anti-HIV antibody) and is separatedfrom the supernatant fluid, and the immune complex or the supernatantfluid are detected, as by radioactive counting, addition of an enzymesubstrate, and color development, or by inclusion of a chemical label(e.g., colloidal gold, latex beads, etc.).

The present invention particularly relates to the use ofimmuno-chromatographic assay formats to detect anti-HIV antibodies. In apreferred immunochromatographic assay format, two contacting, butspatially distinct, porous carriers are employed. The first such carrierwill contain a non-immobilized, labeled peptide of the present inventionand the second such carrier will contain an immobilized, but unlabeledantibody that binds to IgG (e.g., where human anti-HIV antibodies arebeing assayed, the unlabeled antibody may be an anti-human IgGantibody). Preferably, the device will comprise a hollow casingconstructed of, for example, a plastic material, etc., in which thefirst carrier will communicate indirectly with the interior of thecasing via a multilayer filter system that is accessible from the device(e.g., by protruding therefrom or by being incompletely covered by thedevice), such that a serum, plasma, or whole blood test sample can beapplied directly to the filter system and will permeate therefrom intothe first porous carrier. In such a device, the permeation of fluidcontaining anti-HIV antibodies will cause the non-immobilized labeledpeptide of the first carrier to become bound to the migratingantibodies, and will then permeate into the second carrier. Because thesecond carrier contains immobilized antibody that binds human IgG, anylabeled peptide entering the second carrier will be entrapped therein.Detection of labeled peptide in the carrier containing the immobilizedunlabeled antibody thus indicates that anti-HIV antibodies were presentin the sample being evaluated. The assay can be made quantitative bymeasuring the quantity of labeled peptide that becomes bound within thesecond porous carrier.

Having now generally described the invention, the same will be morereadily understood through reference to the following examples, whichare provided by way of illustration, and are not intended to be limitingof the present invention, unless specified.

Example 1 Identification of New Serologic Epitopes

In order to identify new serologic epitopes that conform to the abovediscussed criteria, gene-fragment phage display libraries areconstructed by limited DNase 1 digestion of HIV-1 DNA (NL4-3 clone) togenerate random DNA fragments, 50-300 bp long. The fragments arepurified and polished with T4 DNA polymerase and cloned at the N-terminiof the coat protein of phage display vectors (FIG. 1). This procedureresults in the formation of a phage library that contains every possibleencoded peptide in any of the reading frames.

The library is subjected to panning on immobilized serum antibodies fromHIV-1-infected individual (early seroconversion). Phages that bind tothe immobilized antibodies are retained, while non-binding, or weaklybinding, phages are washed-off (FIG. 2).

DNA sequencing of the captured phages (after amplification in andindividual separation in E. coli) allows the mapping of the selectedpeptides to known HIV proteins. Initially, 11 “phagotopes” were selectedand sequenced. They map to GAG-p6, RT, IN, Vif, gp120, gp41, and Nef.These sequences are produced as synthetic peptides.

Further screenings were conducted with 5 panels of sequential sera fromHIV-1 seroconvertors (provided by Boston Biomedica Inc.). Four of theinitial 11 epitopes are found to interact with early post-infectionsera, demonstrating medium to high binding affinity. They map to GAG-p6,gp120, gp41, and Nef. Furthermore, in extended screens of random HIVseropositive plasma samples, these peptides are found to be reactivewith 80-99% of all seropositive plasma tested. No false reactivity isdetected with 100 sera from seronegative individuals.

Based on the above-described results, it is concluded that a combinationof 1, 2, or more of the selected peptides are useful in the detection ofbreakthrough infections in the context of HIV vaccine trials. Sequencealignment of 3 selected peptides (from GAG-p6, gp41, and Nef) withconsensus sequences for all clades in the Los Alamos database, reveals ahigh degree of conservation (FIG. 3).

Example 2 Production and Use of New Serologic Epitopes

Large quantities of highly purified synthetic peptides expressing theidentified sequences from HIV-1 GAG-p6, gp41, and Nef, or HIV-2 Gag-p6and gp36, are produced under GLP conditions. The synthetic peptides areused to coat ELISA plates.

The reactivities of the synthetic peptides are tested with earlyseroconversion samples from different countries and different clades(under standardized conditions). Pre-clinical and clinical samples ofimmune sera from recent HIV vaccine candidates, likely to proceed tophase I/II/III trials, are screened in order to confirm and expand theabove-described demonstration of the ability of the newly discoveredHIV-1 epitopes, either alone or in combination, to react with highpercentage of plasma from early seroconversion-patients. Currentlylicensed EIA kits may be used for side-by-side analysis.

The reactivity of immune sera from recipients of complex HIV vaccinecandidates (as well as from pre-clinical studies of these vaccines)should be negative.

If plasma from Africa or Asia are not uniformly reactive with the GladeB epitopes, they should score positive on consensus peptides. Inaddition, new Gene-fragment phage-display libraries can be constructedusing HIV genomes from other clades.

The selected peptides in combination can be used to differentiatebetween vaccine directed antibodies and breakthrough infection generatedantibodies during HIV vaccine clinical trials.

Example 3 HIV ELISA

In order to determine preferred conditions for conducting an ELISA usingthe peptides of the present invention, various combinations of peptides,coating amounts, blocking agents, serum/plasma dilutions, secondantibodies, second antibody dilutions and substrates are tested (a feware summarized in Table 11). ELISAs are characterized for the followingsample types: normal (non-HIV infected) serum samples (for cut-offdetermination); confirmed HIV infected serum samples; seroconversionsamples, serum samples from patients infected with different HIV-1subtypes, randomly collected serum samples-blinded panel, vaccinatedindividual serum samples. ELISAs are also characterized forcross-reactivity with other pathogens including reteroviruses.

From such characterizations preferred assay conditions are found toemploy a peptide for epitope presentation, a coating of 33 ng (forGAG-p6) or 250 ng (for ENV-gp-41), blocking by 2% milk, a 1:100serum/plasma dilution, a HRP-Anti-Human IgG-Fc as the 2^(nd) antibody(at 1:10,000 fold dilution), and OPD as substrate. Buffers employed maybe common buffers such as PBS or Tris buffer, with or without Tween-20or other detergents commonly used for immunoassays. All incubations aredone at room temperature for 1 hr each, except for blocking by milk,which is done for 2-3 hrs. The peptides employed are the GAG-p6 (SEQ IDNO:3) and gp41 (SEQ ID NO:50 and SEQ ID NO:55)), alone and incombination. These assay conditions are employed in the ELISAs describedin the examples provided below, unless otherwise indicated.

FIG. 4 shows the frequency of negative samples (n=600) obtained inELISAs employing the GAG-p6 (SEQ ID NO:3; Panel A) and gp41 (SEQ IDNO:50 and SEQ ID NO:55); Panel B) peptides, alone and in combination(Panel C). For the GAG-p6 ELISA results shown in FIG. 4, panel A, theaverage optical density (OD) was 0.018, the standard deviation (SD) was0.024, and the calculated cut-off was the average optical density+3×SD(=0.137). The actual cut-off used was 0.15. For the gp41 ELISA resultsreported in FIG. 4, Panel B, the average optical density (OD) was 0.005,the standard deviation (SD) was 0.0025, and the calculated cut-off wasthe average optical density+3×SD (=0.0173). The actual cut-off used was0.035. For these ELISAs, the Specimen/Cut-Off Ratio is defined as theAbsorbance of the Test Sample divided by the actual Cut-Off Value. Ifthe Specimen/Cut-Off Ratio is greater than or equal to 1, the sample isscored as positive for the presence of anti-HIV antibodies, and istermed “HIV positive.” If the Specimen/Cut-Off Ratio is less than 1, thesample is scored as negative for the presence of anti-HIV antibodies,and is termed “HIV negative.”

Using the above-described preferred assay conditions, theSpecimen/Cut-Off Ratio was determined for an HIV+ serum sample at timesranging from 0 to 40 days. The results of this experiment are shown inTable 12. In Table 12, Abbott HIV 1/2 is a licensed HIV serodetectionkit. HIV Ag is a licensed kit to detect p24. Data relating to FDAlicensed EIA Kits was generated by Boston Biomedica Inc (Gaithersburg,USA).

TABLE 12 Day Sample Col- CBER CBER Abbott Abbott FDA LIC. I.D. lected P6gp41 HIV 1/2 HIV Ag EIA KITS PRB-929-01 0 0.56 0.43 0.2 0.5 0/5PRB-929-02 4 0.48 0.4 0.2 0.5 0/5 PRB-929-03 14 0.9 0.56 0.2 0.9 0/5PRB-929-04 18 0.94 0.52 0.2 13.4 0/5 PRB-929-05 21 0.8 0.5 0.9 >22.7 0/5PRB-929-06 25 1.2 0.74 >16.3 >22.7 1/5 PRB-929-07 28 8.41.02 >16.3 >22.7 3/5

The seroreactivity of the peptides during acute infection was evaluated.The results of these ELISAs are shown in Table 13.

TABLE 13 Day Sample Col- CBER CBER Abbott Abbott FDA LIC. I.D. lected p6Gp41 HIV 1/2 HIV Ag EIA KITS PRB910-1 0 0.45 0.32 0.2 0.4 0/5 PRB910-214 0.88 0.57 0.2 5.7 0/5 PRB910-3 26 2.8 0.69 10.4 0.6 5/5 PRB910-4 282.87 0.89 7.4 0.5 5/5 PRB910-5 32 4.66 0.97 7.6 0.4 5/5 PRB910-6 35 4.251.04 7.1 0.4 5/5 PRB910-7 40 3.84 2.01 7.8 0.4 5/5

The analysis of five different seroconversion panels shows that HIV-1infection can be detected using the peptides of the present inventionwithin 2-3 weeks following HIV-1 RNA detection by the polymerase chainreaction (PCR).

Example 4 Early Detection of HIV-1 Infection by Peptides inSeroconversion Panels

The peptides and assays of the present invention are employed using theabove-described ELISA conditions to detect HIV-1 infection in serum fromseroconverted individuals. The data from such assays is shown in Table14.

TABLE 14 Specimen/ ID Day Cut-Off Ratio Sample ID Number Collected p6gp41 AUS-105 PS04017 0 0.51 3.97 8 0.56 5.41 29 0.7 12.33 56 0.87 16.24168 0.88 25.93 259 2.69 29.32 AUS-107 PS01019 0 0.93 3.52 28 1.07 4.9561 0.71 4.97 168 0.78 11.95 AUS-108 PS02016 0 1.73 0.42 12 2.64 0.45 311.24 0.99 66 3.06 4.82 192 0.73 7.89 269 0.77 19.35 AUS-113 PS01026 00.41 12.56 27 0.56 14.91 56 0.73 20.15 166 0.75 21.22 AUS-114 PS01029 02.77 7.4 7 2.12 7.22 28 2.86 7.41 56 7.63 8.18 147 16.19 19.21 AUS-115PM01002 0 0.84 11.49 159 1.37 14.14 AUS-116 PM01003 0 1.11 0.61 7 1.651.32 20 1.32 2.68 55 2.11 11.92 168 1.28 20.92 AUS-117 PM02001 0 1.487.87 7 1.24 7.43 28 1.48 13.61 61 0.8 19.22 169 1.03 23.07 252 0.8221.89 364 0.8 26.58 AUS-118 PM02002 0 16.07 0.81 10 14.17 0.9 25 12.94.82 50 15.8 12.66 170 18.21 27.58 252 15.47 27.33 374 7.9 30.96 AUS-120PM02004 0 1.27 0.71 7 1.21 0.78 36 2.28 1.58 70 5.34 1.98 182 5.47 3.51259 5.48 7.38 AUS-121 PM02006 0 0.57 5.85 9 0.52 4.65 28 0.53 3.74 560.69 4.39 168 0.51 1.76 252 0.54 1.17 AUS-123 PM03001 0 1.93 6.14 181.18 4.53 57 0.76 2.89 87 0.71 2.63

The data demonstrate that the peptides and assays of the presentinvention can be employed to detect HIV-1 infection in serum fromseroconverted individuals.

Example 5 Cross Clade Reactivity of Peptides for HIV-1 Diagnosis

The peptides and assays of the present invention are evaluated using theabove-described ELISA conditions for cross-clade reactivity in theirdetection of HIV-1 infection. The data from such assays is shown inTable 15.

TABLE 15 HIV-1 Sample Geno- Origin Abbott FDA LIC. I.D. type p6 gp41 ofSample HIV 1/2 EIA KITS WWRB303-01 A 6.26 29.17 Ghana >15.9 4/4WWRB303-02 A 18.44 0.53 Ghana >15.9 4/4 WWRB303-03 C 3.24 4.53 S.Africa >15.9 4/4 WWRB303-04 C 5.12 1.09 S. Africa >15.9 4/4 WWRB303-05 D2.90 62.43 Uganda >15.9 4/4 WWRB303-06 D 15.90 2.50 Uganda >15.9 4/4WWRB303-07 G 3.02 0.52 Ghana >15.9 4/4 WWRB303-08 G 1.10 0.23Ivory >15.9 4/4 Coast WWRB303-09 O 0.53 0.31 Spain 2.4 4/4 WWRB303-10 F2.44 0.38 Argentina >15.9 4/4 WWRB303-11 HIV-2 0.03 0.05 Ivory 0.3 2/4Coast WWRB303-12 NEG 0.03 0.07 Argentina 0.4 0/4 WWRB303-13 A 13.6050.17 Uganda >15.9 4/4 WWRB303-14 C 5.37 1.63 Zimbabwe >15.9 4/4WWRB303-15 B 0.73 55.40 U.S.A >15.9 4/4

The data demonstrates that the peptides and assays of the presentinvention exhibit broad cross-clade reactivity in their detection ofHIV-1 infection.

Example 6 Reactivity of Peptides with Random Serum Samples fromindividuals Infected with Diverse HIV-1 Clades

The peptides and assays of the present invention are evaluated using theabove-described ELISA conditions for their ability to detect HIV-1infection using random serum samples from individuals infected withdiverse HIV-1 clades. The data from such assays is shown in Table 16.

TABLE 16 Sample I.D. Subtype p6 gp41 NYU-01 AG^(pro) AG^(gag) A^(env)3.8 91.63 NYU-02 AG^(pro) 17.79 36.96 NYU-03 AG^(pro) AG^(gag) AG^(env)0.75 1.53 NYU-04 AG^(pro) G^(gag) G^(env) 9.24 87.7 NYU-05 AG^(pro)AG^(gag) A^(env) 5.64 53.8 NYU-06 AG^(pro) A^(gag) A^(env) 19.15 91.6NYU-07 J^(pro) 11.76 0.1 NYU-08 A^(pro) 1.84 86.8 NYU-09 AG^(pro)AG^(gag) A^(env) 1.6 45.43 NYU-10 AG^(pro) 1.86 0.47 NYU-11 AG^(pro)7.52 96.57 NYU-12 AG^(pro) 14.78 6.07 NYU-13 AG^(pro) 0.26 95.87 NYU-14AG^(pro) 0.45 6.83 NYU-15 AG^(pro) 1.3 0.33 NYU-16 AG^(pro) AG^(gag)AG^(env) 0.9 88.03 NYU-17 AG^(pro) AG^(gag) AG^(env) 1.56 73.07 NYU-18A^(pro) 0.4 3.73 NYU-19 A^(pro) A^(gag) AG^(env) 5.67 79.27 NYU-20A^(pro) A^(gag) A^(env) 18.56 16.17 NYU-21 AG^(pro) 18.33 91.97 NYU-22A^(pro) A^(gag) A^(env) 1.63 93.43 NYU-23 AG^(pro) 15.05 70.27 NYU-24AG^(pro) 3.86 1.63 NYU-25 AG^(pro) 16.14 73.97 NYU-26 AG^(pro) AG^(gag)A^(env) 20.48 87.27 NYU-27 AG^(pro) 4.68 0.8 NYU-28 AG^(pro) 15.66 87NYU-29 AG^(pro) 7 0.47 NYU-30 AG^(pro) 8.78 84.3 NYU-31 AG^(pro) 2.3387.17 NYU-32 A^(pro) 0.39 1.7 NYU-33 AG^(pro) F2^(gag) F2^(env) 13.6797.67 NYU-34 AG^(pro) AG^(gag) AG^(env) 1.48 72.5 NYU-35 AG^(pro) 4.9615.37 NYU-36 J^(pro) 0.04 56.26 NYU-37 G^(pro) G^(gag) G^(env) 0.5892.37 NYU-38 AG^(pro) 1.23 1.93 NYU-39 AG^(pro) 0.59 0.33 NYU-40AG^(pro) 18.07 89.9 NYU-41 AG^(pro) 10.41 93.43 NYU-42 AG^(pro) 0.6777.73 NYU-43 C^(pro) 1.15 0.57 NYU-44 AG^(pro) AG^(gag) AG^(env) 1.311.03 NYU-45 AG^(pro) 10.73 5.23 NYU-46 A^(pro) AE^(gag) A^(env) 9.6572.7 NYU-47 AG^(pro) 1.71 44.7 NYU-48 AG^(pro) 8.06 90.97 NYU-49AG^(pro) 1.04 86.23 NYU-50 AG^(pro) 2.27 92.6 NYU-51 A^(pro) 4.65 0.67NYU-52 D^(pro) 1.84 94.5 NYU-53 D^(pro) D^(gag) D^(env) 2.3 35.8 NYU-54J^(pro) G^(gag) A^(env) 18.24 93.03 NYU-55 AG^(pro) 3.05 92.83 NYU-56G^(pro) G^(gag) A^(env) 1.96 2 NYU-57 AG^(pro) 15.89 84.8 NYU-58 G^(pro)1.57 8.83 NYU-59 U^(pro) 1.5 68.7 NYU-60 A^(pro) 3.18 95.5 NYU-61A^(pro) 0.58 93 NYU-62 AG^(pro) 6.22 77.97 NYU-63 A^(pro) 1.31 96.1NYU-64 AG^(pro) 11.61 30.3 NYU-65 A^(pro) 0.92 77.53 NYU-66 AG^(pro)AG^(gag) A^(env) 2.24 6.3 NYU-67 AG^(pro) 20.34 7.07 NYU-68 AG^(pro)7.93 49.17 NYU-69 AG^(pro) 2.01 96.2 NYU-70 AG^(pro) AG^(gag) AG^(env)1.29 53.17 NYU-71 AG^(pro) 20.66 9.56 NYU-72 AG^(pro) 3 12.14 NYU-73AG^(pro) 6.27 54.16 NYU-74 A^(pro) 19.21 4.68 NYU-75 AG^(pro) 16.0915.82 NYU-76 AG^(pro) 6.79 54.58 NYU-77 J^(pro) 11cpx^(gag) 11cpx^(env)1.63 11.84 NYU-78 AG^(pro) 6.13 0.1 NYU-79 AG^(pro) 6.12 92.07 NYU-80AG^(pro) 0.37 91.97 NYU-81 G^(pro) 3.87 25.6 NYU-82 D^(pro) 0.38 7.23NYU-83 AG^(pro) 10.1 30.7 NYU-84 H^(pro) 0.87 97.6 NYU-85 AG^(pro)AG^(gag) A^(env) 1.39 2.1 NYU-86 D^(pro) 7.4 1.43 NYU-87 F2^(pro) 0.4986.1 NYU-88 A^(pro) AG^(gag) AG^(env) 16.62 97.47 NYU-89 AG^(pro) 15.9979.2 NYU-90 G^(pro) G^(gag) G^(env) 6.96 95.83 NYU-91 AG^(pro) C^(gag)AG^(env) 1.03 1.03 NYU-92 J^(pro) 11cpx^(gag) A^(env) 1.21 0.77 NYU-93AG^(pro) AG^(gag) AG^(env) 1 97.9 NYU-94 C^(pro) C^(gag) C^(env) 5.240.33 NYU-95 C^(pro) 6.54 1.17 NYU-96 AG^(pro) 0.97 0.06 NYU-97 U^(pro)AG^(gag) A^(env) 1.03 1.22 NYU-98 AG^(pro) 20.6 2.08 NYU-99 AG^(pro)AG^(gag) AG^(env) 3.63 56.8 NYU-100 F2^(pro) F2^(gag) F2^(env) 4.89 40.8

The data shown in Table 16 indicates that the gag p6 epitope had anindividual sensitivity of 83%, compared with 67% for the gp41 epitope.The use of both epitopes had an individual sensitivity of 82%. Theoverall sensitivity was 100%.

Example 7 Reactivity of Peptides Designed Based on HIV-1 SubtypeConsensus Sequences with False Negative Serum Samples

The reactivity of peptides designed based on HIV-1 subtype consensussequences with false negative serum samples (using the HIV subtype-Bbased peptides) is evaluated using the above-described ELISA conditions.The data is shown in Table 17 below.

TABLE 17 Specimen/Cut-Off Ratio Sample ID p6 gp41 Consensus p6 Consensusgp41 NYU-02 18.67 12.86 19.28 22.28 NYU-03 0.96 0.2 3.06 0.31 NYU-140.64 0.19 3.31 0.21 NYU-18 0.83 0.38 1.37 0.18 NYU-32 0.66 0.23 2.150.26 NYU-36 18.14 11.19 17.01 10.04 NYU-39 1.11 0.72 1.31 0.53 NYU-820.65 0.22 0.8 0.32 NYU-96 2.22 0.2 3.94 0.47 CBER Negative 0.49 0.1 0.360.12 CBER Positive 0.09 29.4 0.19 26.28 HIV Ig 7.28 42.53 6.18 36.49

The data shows that peptides designed based on HIV-1 subtype consensussequences with false negative serum could detect HIV infection.

In summary, the data shows that HIV-1 specific peptides individually orin combination are able to detect anti-HIV-1 antibodies in serum orplasma early after acute infection. The assay specificity for the 1200samples obtained from individuals infected with diverse HIV clades isfound to be 98.2% (For Consensus peptide GAG-p6) and 100% (For Consensuspeptide CON-Env2-gp41). The cross Glade combined reactivity is found tobe 94.4% sensitivity (B-subtype) and 99.1% (for Consensus peptides). Thepeptides and assays of the present invention are able to detect HIVepitopes in serum samples infected with diverse HIV-1 subtypes.

Example 8 Reactivity of Peptides with Random Serum Samples

The reactivity of the CBER p6 and CBER gp41 with a wide variety ofdiverse serum samples are shown in Table 18 below.

TABLE 18 SAMPLE CBER CBER ID p6 Gp41 Subtype and Infection StatusNHLBI-1 17.57 0.23 Brazil; clade B; LSI NHLBI-2 0.98 6.22 Brazil; cladeB; LSI NHLBI-3 0.69 13.55 Brazil; clade B; LSI NHLBI-4 1.44 27.58Brazil; clade B; LSI NHLBI-5 7.86 35.23 Brazil; clade B; LSI NHLBI-63.18 0.43 Brazil; clade B; LSI NHLBI-7 7.21 33.97 Brazil; clade B; LSINHLBI-8 4.77 1.75 Brazil; clade B; LSI NHLBI-9 15.90 0.18 Brazil; cladeB; LSI NHLBI-10 6.34 0.35 Brazil; clade B; LSI NHLBI-11 10.56 24.45Brazil; clade B; LSI NHLBI-12 2.63 7.94 Brazil; clade B; LSI NHLBI-131.13 14.96 Brazil; clade B; LSI NHLBI-14 2.03 7.58 Brazil; clade B; LSINHLBI-15 3.18 0.51 Brazil; clade B; LSI NHLBI-16 15.74 6.25 Brazil;clade B; LSI NHLBI-17 2.01 0.30 Brazil; clade B; LSI NHLBI-18 13.1432.63 Brazil; clade B; LSI NHLBI-19 5.52 4.30 Brazil; clade B; LSINHLBI-20 1.14 0.93 Brazil; clade B; LSI NHLBI-21 3.52 12.28 Brazil;clade B; LSI NHLBI-22 10.25 26.03 Brazil; clade B; LSI NHLBI-23 2.910.36 Brazil; clade B; LSI NHLBI-24 6.88 0.20 Brazil; clade B; LSINHLBI-25 3.03 8.89 Brazil; clade B; LSI NHLBI-26 0.95 2.89 Brazil; cladeB; recent NHLBI-27 7.90 1.94 Brazil; clade B; recent NHLBI-28 2.45 0.35Brazil; clade B; recent NHLBI-29 4.73 0.57 Brazil; clade B; recentNHLBI-30 5.21 1.64 Brazil; clade B; recent NHLBI-31 2.60 0.55 Brazil;clade B; recent NHLBI-32 0.73 2.1 Brazil; clade B; recent NHLBI-33 1.630.25 Brazil; clade B; recent NHLBI-34 1.67 1.78 Brazil; clade B; recentNHLBI-35 1.20 1.16 Brazil; clade B; recent NHLBI-36 3.72 0.12 Brazil;clade B; recent NHLBI-37 6.59 0.43 Brazil; clade B; recent NHLBI-38 0.631.40 Brazil; clade B; recent NHLBI-39 4.32 15.82 Brazil; clade B; recentNHLBI-40 1.57 0.31 Brazil; clade B; recent NHLBI-41 3.19 0.43 Brazil;clade B; recent NHLBI-42 15.65 0.77 Brazil; clade B; recent NHLBI-435.44 1.91 Brazil; clade B; recent NHLBI-44 1.13 0.39 Brazil; clade B;recent NHLBI-45 0.89 1.39 Brazil; clade B; recent NHLBI-46 2.86 0.93Brazil; clade B; recent NHLBI-47 1.13 3.13 Brazil; clade B; recentNHLBI-48 6.11 0.37 Brazil; clade B; recent NHLBI-49 0.65 7.13 Brazil;clade B; recent NHLBI-50 1.97 0.50 Brazil; clade B; recent NHLBI-51 0.420.23 US false positive: EIA R; WB ind NHLBI-52 0.31 0.09 US falsepositive: EIA R; WB ind NHLBI-53 0.04 0.10 US false positive: EIA R; WBind NHLBI-54 0.62 0.20 US false positive: EIA R; WB ind NHLBI-55 0.060.13 US false positive: EIA R; WB ind NHLBI-56 0.18 0.13 US falsepositive: EIA R; WB ind NHLBI-57 0.10 0.08 US false positive: EIA R; WBind NHLBI-58 0.44 0.29 US false positive: EIA R; WB ind NHLBI-59 0.230.18 US false positive: EIA R; WB ind NHLBI-60 0.59 0.24 US falsepositive: EIA R; WB ind NHLBI-61 0.18 0.18 US false positive: EIA R; WBind NHLBI-62 0.77 0.23 US false positive: EIA R; WB ind NHLBI-63 0.300.18 US false positive: EIA R; WB ind NHLBI-64 0.04 0.08 US falsepositive: EIA R; WB ind NHLBI-65 0.10 0.10 US false positive: EIA R; WBind NHLBI-66 0.06 0.07 US false positive: EIA R; WB ind NHLBI-67 0.130.21 US false positive: EIA R; WB ind NHLBI-68 0.09 0.18 US falsepositive: EIA R; WB ind NHLBI-69 0.16 0.20 US false positive: EIA R; WBind NHLBI-70 0.11 0.23 US false positive: EIA R; WB ind NHLBI-71 0.100.14 US false positive: EIA R; WB ind NHLBI-72 0.13 0.39 US falsepositive: EIA R; WB ind NHLBI-73 0.80 0.10 US false positive: EIA R; WBind NHLBI-74 0.53 0.19 US false positive: EIA R; WB ind NHLBI-75 0.160.41 US false positive: EIA R; WB ind NHLBI-76 0.04 0.18 US falsepositive: EIA R; WB neg NHLBI-77 0.13 0.13 US false positive: EIA R; WBneg NHLBI-78 0.09 0.16 US false positive: EIA R; WB neg NHLBI-79 0.340.26 US false positive: EIA R; WB neg NHLBI-80 0.10 0.20 US falsepositive: EIA R; WB neg NHLBI-81 0.37 0.18 US false positive: EIA R; WBneg NHLBI-82 0.40 0.28 US false positive: EIA R; WB neg NHLBI-83 0.280.23 US false positive: EIA R; WB neg NHLBI-84 0.36 0.10 US falsepositive: EIA R; WB neg NHLBI-85 0.12 0.55 US false positive: EIA R; WBneg NHLBI-86 0.71 0.65 US false positive: EIA R; WB neg NHLBI-87 0.810.21 US false positive: EIA R; WB neg NHLBI-88 0.28 0.31 US falsepositive: EIA R; WB neg NHLBI-89 0.12 0.20 US false positive: EIA R; WBneg NHLBI-90 0.06 0.37 US false positive: EIA R; WB neg NHLBI-91 0.390.23 US false positive: EIA R; WB neg NHLBI-92 0.38 0.63 US falsepositive: EIA R; WB neg NHLBI-93 0.36 0.53 US false positive: EIA R; WBneg NHLBI-94 0.41 0.28 US false positive: EIA R; WB neg NHLBI-95 0.160.23 US false positive: EIA R; WB neg NHLBI-96 0.74 0.50 US falsepositive: EIA R; WB neg NHLBI-97 0.09 0.40 US false positive: EIA R; WBneg NHLBI-98 0.15 0.20 US false positive: EIA R; WB neg NHLBI-99 0.160.20 US false positive: EIA R; WB neg NHLBI-100 0.09 0.26 US falsepositive: EIA R; WB neg NHLBI-101 0.17 0.11 US HIV uninfected: EIA NR;WB NT NHLBI-102 0.19 0.49 US HIV uninfected: EIA NR; WB NT NHLBI-1030.45 0.56 US HIV uninfected: EIA NR; WB NT NHLBI-104 0.11 0.13 US HIVuninfected: EIA NR; WB NT NHLBI-105 0.11 0.17 US HIV uninfected: EIA NR;WB NT NHLBI-106 0.22 0.17 US HIV uninfected: EIA NR; WB NT NHLBI-1070.35 0.28 US HIV uninfected: EIA NR; WB NT NHLBI-108 0.32 0.43 US HIVuninfected: EIA NR; WB NT NHLBI-109 0.61 0.1 US HIV uninfected: EIA NR;WB NT NHLBI-110 0.26 0.44 US HIV uninfected: EIA NR; WB NT NHLBI-1110.19 0.12 US HIV uninfected: EIA NR; WB NT NHLBI-112 0.41 0.13 US HIVuninfected: EIA NR; WB NT NHLBI-113 0.14 0.33 US HIV uninfected: EIA NR;WB NT NHLBI-114 0.20 0.36 US HIV uninfected: EIA NR; WB NT NHLBI-1150.13 0.31 US HIV uninfected: EIA NR; WB NT NHLBI-116 0.50 0.44 US HIVuninfected: EIA NR; WB NT NHLBI-117 0.26 0.43 US HIV uninfected: EIA NR;WB NT NHLBI-118 0.19 0.30 US HIV uninfected: EIA NR; WB NT NHLBI-1190.21 0.34 US HIV uninfected: EIA NR; WB NT NHLBI-120 0.17 0.36 US HIVuninfected: EIA NR; WB NT NHLBI-121 0.20 0.42 US HIV uninfected: EIA NR;WB NT NHLBI-122 0.20 0.26 US HIV uninfected: EIA NR; WB NT NHLBI-1230.29 0.41 US HIV uninfected: EIA NR; WB NT NHLBI-124 0.15 0.30 US HIVuninfected: EIA NR; WB NT NHLBI-125 0.48 0.84 US HIV uninfected: EIA NR;WB NT NHLBI-126 0.27 0.62 US HIV uninfected: EIA NR; WB NT NHLBI-1270.57 0.11 US HIV uninfected: EIA NR; WB NT NHLBI-128 0.17 0.66 US HIVuninfected: EIA NR; WB NT NHLBI-129 0.37 0.56 US HIV uninfected: EIA NR;WB NT NHLBI-130 0.20 0.34 US HIV uninfected: EIA NR; WB NT NHLBI-1310.23 0.35 US HIV uninfected: EIA NR; WB NT NHLBI-132 0.19 0.39 US HIVuninfected: EIA NR; WB NT NHLBI-133 0.25 0.46 US HIV uninfected: EIA NR;WB NT NHLBI-134 0.19 0.34 US HIV uninfected: EIA NR; WB NT NHLBI-1350.28 0.33 US HIV uninfected: EIA NR; WB NT NHLBI-136 0.08 0.14 US HIVuninfected: EIA NR; WB NT NHLBI-137 0.50 0.36 US HIV uninfected: EIA NR;WB NT NHLBI-138 0.21 0.43 US HIV uninfected: EIA NR; WB NT NHLBI-1390.19 0.29 US HIV uninfected: EIA NR; WB NT NHLBI-140 0.52 0.68 US HIVuninfected: EIA NR; WB NT NHLBI-141 0.23 0.49 US HIV uninfected: EIA NR;WB NT NHLBI-142 0.23 0.19 US HIV uninfected: EIA NR; WB NT NHLBI-1430.24 0.38 US HIV uninfected: EIA NR; WB NT NHLBI-144 0.19 0.42 US HIVuninfected: EIA NR; WB NT NHLBI-145 0.26 0.41 US HIV uninfected: EIA NR;WB NT NHLBI-146 0.15 0.45 US HIV uninfected: EIA NR; WB NT NHLBI-14711.20 0.33 US HIV uninfected: EIA NR; WB NT NHLBI-148 0.37 0.34 US HIVuninfected: EIA NR; WB NT NHLBI-149 0.19 0.30 US HIV uninfected: EIA NR;WB NT NHLBI-150 0.22 0.35 US HIV uninfected: EIA NR; WB NT NHLBI-1510.67 3.34 US; clade B; presumed LSI NHLBI-152 0.47 1.90 US; clade B;presumed LSI NHLBI-153 0.86 13.98 US; clade B; presumed LSI NHLBI-1540.96 21.23 US; clade B; presumed LSI NHLBI-155 0.25 9.07 US; clade B;presumed LSI NHLBI-156 0.25 10.32 US; clade B; presumed LSI NHLBI-1570.20 5.31 US; clade B; presumed LSI NHLBI-158 6.81 0.37 US; clade B;presumed LSI NHLBI-159 0.24 0.28 US; clade B; presumed LSI NHLBI-1600.83 10.63 US; clade B; presumed LSI NHLBI-161 1.28 13.47 US; clade B;presumed LSI NHLBI-162 0.23 3.57 US; clade B; presumed LSI NHLBI-1637.04 0.13 US; clade B; presumed LSI NHLBI-164 0.10 6.87 US; clade B;presumed LSI NHLBI-165 0.24 4.44 US; clade B; presumed LSI NHLBI-1660.20 9.78 US; clade B; presumed LSI NHLBI-167 0.74 3.60 US; clade B;presumed LSI NHLBI-168 1.66 0.40 US; clade B; presumed LSI NHLBI-1690.62 23.03 US; clade B; presumed LSI NHLBI-170 8.35 0.09 US; clade B;presumed LSI NHLBI-171 0.10 36.57 US; clade B; presumed LSI NHLBI-1720.41 1.3 US; clade B; presumed LSI NHLBI-173 0.97 34.2 US; clade B;presumed LSI NHLBI-174 2.25 2.48 US; clade B; presumed LSI NHLBI-1750.93 13.76 US; clade B; presumed LSI NHLBI-176 1 0.46 US; clade B;presumed LSI NHLBI-177 0.38 0.64 US; clade B; presumed LSI NHLBI-1788.93 14.48 US; clade B; presumed LSI NHLBI-179 0.63 15.94 US; clade B;presumed LSI NHLBI-180 0.40 15.36 US; clade B; presumed LSI NHLBI-18118.17 3.13 US; clade B; presumed LSI NHLBI-182 0.47 1.36 US; clade B;presumed LSI NHLBI-183 0.34 12.5 US; clade B; presumed LSI NHLBI-1840.37 1.42 US; clade B; presumed LSI NHLBI-185 0.07 2.00 US; clade B;presumed LSI NHLBI-186 0.07 11.24 US; clade B; presumed LSI NHLBI-1870.17 24.03 US; clade B; presumed LSI NHLBI-188 0.27 10.29 US; clade B;presumed LSI NHLBI-189 1.55 17.98 US; clade B; presumed LSI NHLBI-1900.21 9.35 US; clade B; presumed LSI NHLBI-191 0.14 1.31 US; clade B;presumed LSI NHLBI-192 0.16 2.73 US; clade B; presumed LSI NHLBI-1930.10 24.76 US; clade B; presumed LSI NHLBI-194 11.37 0.24 US; clade B;presumed LSI NHLBI-195 9.84 9.46 US; clade B; presumed LSI NHLBI-1960.60 5.82 US; clade B; presumed LSI NHLBI-197 3.44 1.90 US; clade B;presumed LSI NHLBI-198 18.01 9.06 US; clade B; presumed LSI NHLBI-1990.27 1.49 US; clade B; presumed LSI NHLBI-200 4.10 0.72 US; clade B;presumed LSI NHLBI-201 0.97 1.18 SA (black); clade C; recent NHLBI-2020.54 1.40 SA (black); clade C; recent NHLBI-203 0.48 2.47 SA (black);clade C; recent NHLBI-204 0.67 1.62 SA (black); clade C; recentNHLBI-205 0.81 5.62 SA (black); clade C; recent NHLBI-206 0.55 1.02 SA(black); clade C; recent NHLBI-207 2.37 1.48 SA (black); clade C; recentNHLBI-208 9.02 0.46 SA (black); clade C; recent NHLBI-209 2.73 0.58 SA(black); clade C; recent NHLBI-210 4.04 0.62 SA (black); clade C; recentNHLBI-211 0.30 1.70 SA (black); clade C; recent NHLBI-212 2.41 0.44 SA(black); clade C; recent NHLBI-213 2.49 3.89 SA (black); clade C; recentNHLBI-214 0.73 3.24 SA (black); clade C; recent NHLBI-215 0.88 2.96 SA(black); clade C; recent NHLBI-216 1.07 0.68 SA (black); clade C; recentNHLBI-217 1.57 4.78 SA (black); clade C; recent NHLBI-218 0.35 1.38 SA(black); clade C; recent NHLBI-219 0.31 4.53 SA (black); clade C; recentNHLBI-220 4.71 2.11 SA (black); clade C; recent NHLBI-221 0.40 2.36 SA(black); clade C; recent NHLBI-222 3.97 0.60 SA (black); clade C; recentNHLBI-223 3.34 2.34 SA (black); clade C; recent NHLBI-224 0.90 1.12 SA(black); clade C; recent NHLBI-225 1.94 0.50 SA (black); clade C; recentNHLBI-226 2.57 59.11 SA (black); clade C; LSI NHLBI-227 3.18 0.40 SA(black); clade C; LSI NHLBI-228 0.75 55.56 SA (black); clade C; LSINHLBI-229 1.03 31.31 SA (black); clade C; LSI NHLBI-230 2.13 0.58 SA(black); clade C; LSI NHLBI-231 0.40 16.64 SA (black); clade C; LSINHLBI-232 0.37 51.67 SA (black); clade C; LSI NHLBI-233 2.87 0.90 SA(black); clade C; LSI NHLBI-234 0.17 54.16 SA (black); clade C; LSINHLBI-235 0.43 1.60 SA (black); clade C; LSI NHLBI-236 1.04 0.86 SA(black); clade C; LSI NHLBI-237 2.59 46.40 SA (black); clade C; LSINHLBI-238 1.09 3.51 SA (black); clade C; LSI NHLBI-239 2.26 10.00 SA(black); clade C; LSI NHLBI-240 0.75 21.18 SA (black); clade C; LSINHLBI-241 1.44 1.02 SA (black); clade C; LSI NHLBI-242 0.79 1.06 SA(black); clade C; LSI NHLBI-243 1.40 3.22 SA (black); clade C; LSINHLBI-244 0.53 9.87 SA (black); clade C; LSI NHLBI-245 0.58 3.11 SA(black); clade C; LSI NHLBI-246 15.40 1.84 SA (black); clade C; LSINHLBI-247 1.33 9.62 SA (black); clade C; LSI NHLBI-248 0.31 9.36 SA(black); clade C; LSI NHLBI-249 1.86 47.27 SA (black); clade C; LSINHLBI-250 0.57 20.16 SA (black); clade C; LSI NHLBI-251 2.14 5.42 US(ARC); clade B; recent NHLBI-252 0.66 1.50 US (ARC); clade B; recentNHLBI-253 10.06 1.00 US (ARC); clade B; recent NHLBI-254 1.13 0.58 US(ARC); clade B; recent NHLBI-255 0.60 1.02 US (ARC); clade B; recentNHLBI-256 1.49 5.47 US (ARC); clade B; recent NHLBI-257 3.25 12.07 US(ARC); clade B; recent NHLBI-258 3.86 1.62 US (ARC); clade B; recentNHLBI-259 1.78 25.64 US (ARC); clade B; recent NHLBI-260 1.09 1.58 US(ARC); clade B; recent NHLBI-261 0.18 5.36 US (ARC); clade B; recentNHLBI-262 1.99 15.73 US (ARC); clade B; recent NHLBI-263 6.14 2.02 US(ARC); clade B; recent NHLBI-264 9.39 1.06 US (ARC); clade B; recentNHLBI-265 0.55 0.64 US (ARC); clade B; recent NHLBI-266 1.68 30.49 US(ARC); clade B; recent NHLBI-267 1.09 0.56 US (ARC); clade B; recentNHLBI-268 1.50 0.48 US (ARC); clade B; recent NHLBI-269 3.43 7.08 US(ARC); clade B; recent NHLBI-270 0.43 4.11 US (ARC); clade B; recentNHLBI-271 0.50 3.56 US (ARC); clade B; recent NHLBI-272 0.27 1.12 US(ARC); clade B; recent NHLBI-273 1.03 0.74 US (ARC); clade B; recentNHLBI-274 5.41 13.78 US (ARC); clade B; recent NHLBI-275 1.06 2.20 US(ARC); clade B; recent NHLBI-276 3.55 2.64 US (ARC); clade B; recentNHLBI-277 18.51 55.93 US (ARC); clade B; recent NHLBI-278 0.56 0.30 US(ARC); clade B; recent NHLBI-279 1.82 17.11 US (ARC); clade B; recentNHLBI-280 0.64 4.96 US (ARC); clade B; recent NHLBI-281 1.20 1.62 US(ARC); clade B; recent NHLBI-282 9.25 0.42 US (ARC); clade B; recentNHLBI-283 0.39 1.20 US (ARC); clade B; recent NHLBI-284 1.85 0.47 US(ARC); clade B; recent NHLBI-285 0.29 5.87 US (ARC); clade B; recentNHLBI-286 0.52 4.00 US (ARC); clade B; recent NHLBI-287 0.83 1.16 US(ARC); clade B; recent NHLBI-288 2.60 2.70 US (ARC); clade B; recentNHLBI-289 2.54 0.44 US (ARC); clade B; recent NHLBI-290 1.90 1.36 US(ARC); clade B; recent NHLBI-291 4.04 22.56 US (ARC); clade B; recentNHLBI-292 0.41 1.50 US (ARC); clade B; recent NHLBI-293 3.22 3.18 US(ARC); clade B; recent NHLBI-294 0.80 1.64 US (ARC); clade B; recentNHLBI-295 1.28 0.37 US (ARC); clade B; recent NHLBI-296 1.04 1.22 US(ARC); clade B; recent NHLBI-297 7.88 0.76 US (ARC); clade B; recentNHLBI-298 1.55 8.62 US (ARC); clade B; recent NHLBI-299 2.15 0.64 US(ARC); clade B; recent NHLBI-300 1.36 0.47 US (ARC); clade B; recent

Table 19 summarizes the ability of the HIV-SELECTEST to detectHIV-infected serum with diverse clades.

TABLE 19 Summary of HIV-SELECTEST with HIV-Infected Serum Samples withDiverse Clades HIV- Number of SELECTEST % Combined Subtype SamplesReactive Sensitivity A 25 25 100 B 263 259 98.48 C 50 50 100 D 20 19 95E 104 103 99.04 G 11 11 100 J 4 4 100 AG 150 150 100 AJ 7 7 100 F2, U,H, J/G 9 9 100 Recombinants CRF 21 21 100 Unknown Genotypes 589 58599.32 Total No. Samples 1253 1243 99.2

Example 8 Reactivity of Peptides with RV124 Vaccine Trial Samples: aComparison with the BioRad Kit

The reactivity of CBER p6 and CBER p41 with RV124 vaccine trial sampleswere compared with the reactivity of the BioRad Kit with RV124 vaccinetrial samples at 0 and 182 days post-vaccination. The vaccination givenin the RV124 vaccine trials was as follows: ALVAC-HIV (νCP205;gag-LAI+pro-LAI+gp120MN/gp41TM-LAI) with HIV-1 gp160 protein boost(gp120MN, gp41 LAI-2) (with Gag-p6). The results for individual samplesare shown in Table 20 below. The results show substantially more falsepositive reactions using the BioRad kit versus the use of CBER p6 orCBER p41.

TABLE 20 Reactivity Of RV-124 Clinical Trial Samples In The‘HIV-Selectest’ Day 0 Day 182 Day 0 Day 182 HIV BioRad BioRad SERUM NewHIV ELISA′ New HIV ELISA′ INFECTION HIV-1/2 HIV-1/2 SAMPLE p6 gp41 p6gp41 STATUS plus O plus O RV124-1 0.09 0.15 0.36 0.21 NEGATIVE 0.1411.42 RV124-2 0.08 0.10 0.18 0.19 NEGATIVE 0.12 11.14 RV124-3 0.32 0.150.61 0.28 NEGATIVE 0.15 11.45 RV124-4 0.16 0.15 0.35 0.18 NEGATIVE 0.1411.40 RV124-5 0.11 0.16 0.17 0.13 NEGATIVE 0.16 11.08 RV124-6 0.10 0.140.14 0.15 NEGATIVE 0.16 11.78 RV124-7 0.11 0.18 0.12 0.20 NEGATIVE 0.2411.96 RV124-8 0.39 0.22 0.33 0.14 NEGATIVE 0.23 12.01 RV124-9 0.13 0.130.16 0.13 NEGATIVE 0.27 11.72 RV124-10 0.10 0.12 0.13 0.13 NEGATIVE 0.1311.69 RV124-11 0.15 0.18 0.25 0.28 NEGATIVE 0.46 10.93 RV124-12 0.090.08 0.22 0.19 NEGATIVE 0.47 11.38 RV124-13 0.37 0.09 0.59 0.22 NEGATIVE0.14 11.54 RV124-14 0.16 0.19 0.26 0.18 NEGATIVE 0.11 11.19 RV124-150.19 0.10 0.25 0.16 NEGATIVE 0.10 11.51 RV124-16 0.16 0.16 0.20 0.19NEGATIVE 0.13 1.97 RV124-17 0.09 0.05 0.17 0.10 NEGATIVE 0.17 11.38RV124-18 0.30 0.08 0.43 0.16 NEGATIVE 0.13 11.65 RV124-19 0.26 0.13 0.040.09 NEGATIVE 0.20 12.17 RV124-20 0.21 0.10 0.19 0.10 NEGATIVE 0.2011.96 RV124-21 0.16 0.07 0.18 0.10 NEGATIVE 0.22 11.31 RV124-22 0.300.23 0.67 0.43 NEGATIVE 0.27 11.13 RV124-23 0.94 0.15 0.41 0.22 NEGATIVE0.37 0.24 RV124-24 0.15 0.11 0.51 0.42 NEGATIVE 0.48 11.04 RV124-25 0.440.09 0.48 0.21 NEGATIVE 0.15 11.53 RV124-26 0.09 0.08 0.41 0.22 NEGATIVE0.14 11.26 RV124-27 0.24 0.42 0.34 0.47 NEGATIVE 0.14 11.71 RV124-280.14 0.11 0.32 0.20 NEGATIVE 0.15 11.96 RV124-29 0.16 0.79 13.53 0.50NEGATIVE 0.19 11.68 RV124-30 0.80 0.15 0.22 0.17 NEGATIVE 0.15 11.56RV124-31 0.17 0.14 0.24 0.17 NEGATIVE 0.27 12.00 RV124-32 0.20 0.15 0.280.14 NEGATIVE 0.21 11.89 RV124-33 0.43 0.29 0.37 0.18 NEGATIVE 0.3011.59 RV124-34 0.05 0.06 0.43 0.17 NEGATIVE 0.31 11.40 RV124-35 0.040.03 1.56 0.27 NEGATIVE 0.59 0.11 RV124-36 0.13 0.10 0.77 0.37 NEGATIVE0.52 11.55 RV124-37 0.23 0.28 0.26 0.29 NEGATIVE 0.13 0.13 RV124-38 0.310.38 0.45 0.33 NEGATIVE 0.12 11.12 RV124-39 0.31 0.20 0.47 0.19 NEGATIVE0.11 11.64 RV124-40 0.27 0.16 0.54 0.22 NEGATIVE 0.15 11.42 RV124-410.30 0.18 0.43 0.19 NEGATIVE 0.38 10.64 RV124-42 0.37 0.23 0.96 0.20NEGATIVE 0.21 10.65 RV124-43 0.53 0.21 0.50 0.24 NEGATIVE 0.26 0.14RV124-44 0.18 0.37 0.13 0.23 NEGATIVE 0.24 10.95 RV124-45 0.10 0.36 0.080.22 NEGATIVE 0.31 10.99 RV124-46 0.20 0.18 0.15 0.10 NEGATIVE 0.4110.13 RV124-47 0.41 0.20 0.99 0.17 NEGATIVE 0.35 10.81 RV124-48 0.320.19 0.75 0.17 NEGATIVE 0.33 10.40 RV124-49 0.67 0.30 0.47 0.16 NEGATIVE0.35 0.14 RV124-50 0.63 0.18 0.43 0.11 NEGATIVE 0.35 10.55 RV124-51 0.220.09 0.99 0.09 NEGATIVE 0.46 10.43 RV124-52 0.87 0.33 0.23 0.27 NEGATIVE0.32 10.68 RV124-53 0.63 0.18 0.52 0.25 NEGATIVE 0.20 11.07 RV124-540.26 0.13 0.53 0.13 NEGATIVE 0.15 1.17 RV124-55 0.27 0.14 0.27 0.12NEGATIVE 0.16 0.19 RV124-56 0.85 0.11 0.98 0.20 NEGATIVE 0.15 10.89RV124-57 0.36 0.29 0.74 0.25 NEGATIVE 0.17 0.48 RV124-58 0.23 0.20 0.730.20 NEGATIVE 0.22 10.90 RV124-59 0.40 0.37 0.45 0.20 NEGATIVE 0.22 0.53RV124-60 0.71 0.25 0.12 0.36 NEGATIVE 0.20 10.66 RV124-61 0.67 0.18 0.660.11 NEGATIVE 0.19 0.36 RV124-62 0.52 0.47 0.43 0.37 NEGATIVE 0.16 0.15RV124-63 0.01 0.07 0.64 0.35 NEGATIVE 0.21 10.30 RV124-64 0.16 0.08 0.100.12 NEGATIVE 0.26 0.17 RV124-65 0.13 0.30 0.21 0.18 NEGATIVE 0.23 0.19RV124-66 0.26 0.23 0.24 0.24 NEGATIVE 0.19 0.18 RV124-67 0.64 0.20 0.410.10 NEGATIVE 0.19 10.52 RV124-68 0.48 0.29 0.44 0.21 NEGATIVE 0.26 0.27RV124-69 0.30 0.17 0.17 0.11 NEGATIVE 0.18 0.39 RV124-70 0.31 0.25 0.300.11 NEGATIVE 0.16 10.86 RV124-71 0.37 0.18 0.45 0.18 NEGATIVE 0.2110.45 RV124-72 0.32 0.19 0.84 0.15 NEGATIVE 0.23 9.66 RV124-73 0.41 0.230.63 0.11 NEGATIVE 0.22 9.97 RV124-74 0.32 0.23 0.28 0.31 NEGATIVE 0.2110.45 RV124-75 0.27 0.08 0.44 0.12 NEGATIVE 0.22 9.37 RV124-76 0.47 0.160.47 0.20 NEGATIVE 0.31 10.95 RV124-77 0.49 0.10 0.37 0.29 NEGATIVE 0.1710.67 RV124-78 0.04 0.24 0.07 0.20 NEGATIVE 0.15 5.88 RV124-79 0.32 0.200.25 0.18 NEGATIVE 0.15 0.14

Example 8 Reactivity of Peptides with VRC-004 & VRC-006 Vaccine TrialSamples: A Comparison With the BioRad Kit

The reactivity of CBER p6 and CBER p41 with VRC-004 and VRC-006 vaccinetrial samples are compared with the reactivity of the BioRad Kit withVRC-004 and VRC-006 vaccine trial samples. The results are shown inTable 21 below. The results show substantially more false positivereactions using the BioRad kit versus the use of CBER p6 or CBER p41.

TABLE 21 HIV INFECTION SAMPLE ID p6 gp41 STATUS FDA LICENSED EIA VRC-004trial-4 PLASMIDS-pGag-Pol-Nef + pEnv A, pEnv B + pEnv C 004-001-05 0.070.1 Negative (−) Negative (−) 004-002-05 0.03 0.1 Negative (−) Negative(−) 004-003-08 0.01 15.73 Positive (+) Negative (−) 004-004-05 0.05 0.07Negative (−) Negative (−) 004-005-05 0.02 0.1 Negative (−) Negative (−)004-006-05 0.02 0.07 Negative (−) Negative (−) 004-007-05 0.03 0.07Negative (−) Negative (−) 004-008-05 0.07 0.1 Negative (−) Negative (−)004-009-05 0.03 0.07 Negative (−) Positive (+) 004-010-05 0.04 0.1Negative (−) Positive (+) 004-011-05 0.05 0.13 Negative (−) Negative (−)004-012-05 0.03 0.03 Negative (−) Positive (+) 004-013-05 0.03 0.07Negative (−) Negative (−) 004-014-05 0.03 0.13 Negative (−) Negative (−)004-015-05 0.04 0.1 Negative (−) Negative (−) 004-016-05 0.04 0.1Negative (−) Negative (−) 004-017-05 0.05 0.1 Negative (−) Negative (−)004-018-05 0.03 0.1 Negative (−) Negative (−) 004-019-05 0.04 0.2Negative (−) Negative (−) 004-020-05 2.51 1.13 Positive (+) Positive (+)004-021-05 0.01 0.03 Negative (−) Negative (−) 004-022-05 0.02 0.13Negative (−) Negative (−) 004-023-05 0.01 0.03 Negative (−) Negative (−)004-024-05 0.03 0.2 Negative (−) Positive (+) 004-025-05 0.03 0 Negative(−) Positive (+) 004-026-05 0.1 0.23 Negative (−) Negative (−)004-027-05 0.02 0.13 Negative (−) Negative (−) 004-028-05 0.02 0.1Negative (−) Negative (−) 004-029-05 0.05 0.1 Negative (−) Negative (−)004-030-05 0.03 0.07 Negative (−) Negative (−) 004-031-05 0.21 0.13Negative (−) Negative (−) 004-032-05 0.01 0.07 Negative (−) Negative (−)004-033-05 0.03 0.1 Negative (−) Negative (−) 004-034-05 0.01 0.07Negative (−) Negative (−) 004-035-05 0.03 0.13 Negative (−) Positive (+)004-036-05 0.04 0.1 Negative (−) Positive (+) 004-037-05 0.05 0.07Negative (−) Positive (+) 004-038-05 0.05 0.03 Negative (−) Positive (+)004-039-05 0.19 0.03 Negative (−) Negative (−) 004-040-05 0.05 0.13Negative (−) Positive (+) 004-041-05 0.02 0.07 Negative (−) Negative (−)004-042-05 0.61 0.07 Negative (−) Negative (−) 004-043-05 0.11 0.03Negative (−) Negative (−) 004-044-05 0.06 0.03 Negative (−) Negative (−)004-045-05 0.04 0.03 Negative (−) Negative (−) 004-046-05 0.12 0.13Negative (−) Negative (−) 004-047-05 0.05 0.03 Negative (−) Negative (−)004-048-05 0.06 0.1 Negative (−) Negative (−) 004-049-05 0.13 0.13Negative (−) Negative (−) 004-050-05 0.03 0.03 Negative (−) Negative (−)VRC-006 trial-4 Ad5-Ad5-Gag-Pol + Ad5-Env A, Ad5-Env B + Ad5-Env C006-001-03 0.19 0.2 Negative (−) Negative (−) 006-002-03 0.01 −0.07Negative (−) Negative (−) 006-003-03 0.44 0.1 Negative (−) Negative (−)006-004-03 0.03 0.13 Negative (−) Positive (+) 006-005-03 0.01 0.07Negative (−) Negative (−) 006-006-03 0.04 0.07 Negative (−) Negative (−)006-007-03 0.05 0.17 Negative (−) Negative (−) 006-008-03 0.01 0.1Negative (−) Negative (−) 006-009-03 0.02 0.1 Negative (−) Negative (−)006-010-03 0.04 0.07 Negative (−) Positive (+) 006-011-03 0.04 0.07Negative (−) Positive (+) 006-012-03 0.02 0.03 Negative (−) Negative (−)006-013-03 0.03 0.07 Negative (−) Negative (−) 006-014-03 0.01 0.03Negative (−) Positive (+) 006-015-03 0.28 0.1 Negative (−) Positive (+)006-016-03 0.07 0.07 Negative (−) Positive (+) 006-017-03 0.03 0.07Negative (−) Negative (−) 006-018-03 0.01 0.03 Negative (−) Positive (+)006-019-03 0.03 0.03 Negative (−) Positive (+) 006-020-03 0.05 0.1Negative (−) Positive (+) 006-021-03 0.01 0.03 Negative (−) Negative (−)006-022-03 0.03 0.07 Negative (−) Negative (−) 006-023-03 0.04 0.1Negative (−) Negative (−) 006-024-03 0.1 0.07 Negative (−) Negative (−)006-025-03 0.05 0.1 Negative (−) Negative (−) 006-026-03 0.03 0.13Negative (−) Positive (+) 006-027-03 0.01 0.07 Negative (−) Positive (+)006-028-03 0.07 0.2 Negative (−) Positive (+) 006-029-03 0.03 0.1Negative (−) Positive (+) 006-030-03 0.05 0.13 Negative (−) Negative (−)006-031-03 0.03 0.13 Negative (−) Positive (+) 006-032-03 0.03 0.1Negative (−) Positive (+) 006-033-03 0.02 0.07 Negative (−) Positive (+)006-034-03 0.03 0.1 Negative (−) Positive (+) 006-035-03 0.03 0.13Negative (−) Negative (−) 006-036-03 0.02 0.13 Negative (−) Positive (+)SUMMARY 1/86 2/86 2/86 29/86

Example 9 The “HIV-SELECTEST” A New HIV-1 Detection Assay

The present invention provides a new HIV-1 detection assay, in whichvaccine-generated antibodies will not cross-react, while seroconversioncan be detected early post-infection. The selection criteria for HIVsequences to be used in such an assay included epitopes that are: 1) notincluded in HIV vaccines, 2) recognized by antibodies early after HIVinfection, and 3) highly conserved among HIV clades and subtypes.

To identify such sequences, a Gene-Fragment Phage Display Library wasconstructed from the entire HIV-1 genome and used for screening of serafrom HIV-infected individuals around the time of seroconversion. Asdiscussed above, this strategy led to the discovery of three novelepitopes, one in Gag p6 and two in the gp41 cytoplasmic tail. Thedevelopment of a new HIV enzyme-linked immunosorbent assay, termedHIV-SELECTEST, which distinguishes between HIV infected individuals anduninfected vaccine recipients is described below. HIV-SELECTEST is a lowcost, high throughput assay that could be implemented in clinical sitesand blood collection centers worldwide, and serve as an importantdiagnostic tool in HIV vaccine trials.

Methods Construction of a Complete HIV Genome Gene-Fragment PhageDisplay Library

Plasmid pNL4-3, containing the complete HIV-1 NL4-3 proviral DNA wasobtained from the NIH AIDS Research and Reference Reagent Program(McKesson BioServices Corp., Rockville, Md.). Full length HIV-1 genomewas PCR amplified from pNL4-3 DNA with the Expand long templatepolymerase preparation (Roche Diagnostics, Indianapolis, Ind.) andprimers spanning the Lys t-RNA primer binding site (MSF12, (SEQ IDNO:139) 5′-AAAAATCTCTAGCAGTGGCGCCCGAACAG-3′) and the poly-A signalregion of 3′-LTR (MSR5, (SEQ ID NO:140)5′-AAGCACTCAAGGCAAGCTTTATTGAGGCT-3′), which amplifies the entire HIV-1genome except for 75 bp in the unique-5′ (U5) region of the LTR. Thepurified amplified DNA product was digested with DNase I using DNaseshotgun cleavage kit (Novagen, Madison, Wis.), and fragments between 50and 300 bp were isolated by preparative gel electrophoresis, treatedwith T4 DNA polymerase to generate blunt ends, and dephosphorylatedusing calf intestinal alkaline phosphatase (CIP) (Roche Diagnostics,Indianapolis, Ind.). DNA was again purified using nucleotide removal kit(Qiagen Inc, Valencia, Calif.) and was ligated in the presence of Srf Ienzyme into the Sma I site of the M13 derived phage vector forexpression as gIIIp fusion protein, followed by electroporation into E.coli TGI cells. Tet-resistant transformants were harvested and expandedin liquid culture (2X-YT) at 37° C. The cell-free phage supernatant wasisolated by centrifugation and phage titer was determined as Teetransduction units. Ninety six individual clones were isolated and DNAinserts were amplified by standard PCR and sequenced to determine theinsert size distribution and library diversity.

Selection of Phages Reactive with HIV Antibodies from Early InfectedIndividuals

Seven plasma samples constituting the HIV-1 seroconversion panel PRB-910from SeraCare BioServices (Gaithersburg, Md.) were used for panning ofthe HIV-1 gene-fragment phage display library (GFPDL). For removal ofplasma components, which could non-specifically interact with phageproteins, 5-fold diluted plasma was pre-adsorbed three times on sterilepolystyrene Petri dishes (35 mm diameter) coated with 10¹³ UV-killedVCSM13. For biopanning, the microtiter strips (NUNC Inc, Naperville,Ill.) were coated with a mixture of 500 ng each of goat anti-humanIgG-Fc and goat anti-human IgM-Fc specific antibodies in PBS, pH 7.4.After three washings with PBST (20 mM PBS containing 0.1% Tween 20),DMEM containing 5% FBS (blocking solution) was added to wells to blockthe unoccupied reactive sites. VCSM13 pre-adsorbed HIV-1 human plasmawas added to the wells and incubated for 1 h at room temperature (RT).Wells were washed thrice with PBST and 10¹⁰ phages per well of the HIV-1GFPDL, diluted in blocking solution, were added for 2 h at RT. Theunbound phages were removed in twelve washes with PBST followed by threewashes with PBS. Bound phages were eluted by addition of 0.1 N HClcontaining BSA (1 mg/ml), for 10 min at RT, and neutralized by adding 8μl of 2 M Tris solution per 100 μA eluate. Four rounds of affinityselection were carried out with each individual serum sample comprisingthe HIV seroconversion panel PRB-910.

Analysis of Affinity Selected Phage Clones

Twenty two phage clones enriched after four rounds of biopanning on eachPRB-910 plasma sample were further screened for specific recognition byHIV seropositive sera and absence of reactivity with seronegative serain affinity-capture phage ELISA. The wells of ELISA plates (Immulon 2HB,Thermo Labsystems, Franklin, Mass.) were coated with 100 ng/well ofanti-phage antibody (GE Healthcare, Piscataway, N.J.), and blocked withDMEM/5% FBS. Subsequently, 10¹⁰ phages of the selected clones were addedper well and incubated for 1 h at RT. Serially diluted sera (in DMEM/5%FBS) were added to the 96-well plates in duplicate and incubated at RTfor 1 h. The bound antibodies were probed with HRP-conjugated goatanti-human IgG-IgM antibodies and the reactions were developed with OPDsubstrate solution (Pierce Biotechnology, Rockford, Ill.). The clonesdemonstrating the best differential reactivity with HIV-1 seropositivesera were expanded and the inserts were sequenced and mapped toindividual HIV-1 genes. Several inserts were selected for syntheticpeptide synthesis and development of the HIV-SELECTEST.

Peptides Used in New HIV-SELECTEST

Peptide sequences from Gag-p6 (SEQ ID NO:3;452-SRPEPTAPPAESFRFGEEITPTPSQKQEPKDKELYPPLASLRSLFGNDPSSQ-502) and gp41cytoplasmic region (SK1; SEQ ID NO:50;784-LIAARIVELLGHSSLKGLRRGWEALKYLWNLLQYWGQELKNSAISL-829 and SK2; SEQ IDNO:55; 836-AVAEGTDRVIEVVQRVCRAILNIPRRIRQGFERALL-871) were chemicallysynthesized (amino acid residues are numbered based on the CON—OF—CONSalignment sequence in the Los Alamos database). All peptides weresynthesized at the Facility for Biotechnology Resources, CBER, FDA, onApplied Biosystems peptide synthesizer models 431 and 433 (Foster City,Calif.) by standard 9-fluorenyl methoxycarbonyl chemistry (Fmoc).Peptides were purified by reverse-phase high performance liquidchromatography (RP-HPLC) and characterized by mass spectrometry(MALDI-TOF MS).

HIV-SELECTEST

Based on preliminary screening of HIV seronegative and seropositivesera, the optimal conditions for the p6 and gp41 ELISA were determined.The p6 peptide was coated at 30 ng/100 μl/well while the gp41 peptides(SEQ ID NO:50 and SEQ ID NO:55) were coated at 150 ng/100 μl/well each(total 300 ng/well) on Immulon-2HB plates. After three washes with PBST(20 mM PBS, 0.1% Tween-20), the unoccupied reactive sites were blockedby PBST containing 2% whole milk (2% WMPBST). All specimens (serum orplasma) were diluted 1:100 in 2% WMPBST, added to peptide-coated wells,and incubated for 1 h at RT. The plates were then washed six times withPBST and 100 Owen of HRP-conjugated goat anti-Human IgG Fe-specificantibody (Jackson ImmunoResearch, West Grove, Pa.), diluted 1:10,000 in2% WMPBST was added. The reactions were quantified usingO-Phenylenediamine (OPD) substrate.

Based on the results with 1000 seronegative samples, cut-off values weredetermined for p6 and gp41 peptides individually. The cut-off valuesused are the average absorbance of Negative sera+5 Standard Deviations(for each peptide). Specimens with an Absorbance/Cut-off ratios of ≧1are considered HIV-1 seropositive and those with ratios<1 are consideredHIV-1 seronegative.

HIV Seroconversion Panels and Vaccine Trial Samples

HIV-1 seroconversion panels PRB-910, PRB-924, PRB-927, PRB-928, PRB-929,PRB-931 and mixed titer panel PRB-204 were purchased from SeraCareBioServices, (Gaithersburg, Md.). A seroconversion panel consists ofplasma samples collected serially early after HIV-1 infection, and thevirological and immunological profiles as assessed by commercialdiagnostic kits for these plasma samples were provided by SeraCareBioServices. Additionally, twenty eight seroconversion panels wereprovided by the University of New South Wales (PHAEDRA Inventory,Sydney, Australia). HIV negative serum samples were obtained fromNational Institutes of Health Blood Bank and the Vaccine Research Center(VRC, NIAID, NIH, Bethesda, Md.).

Serum/Plasma samples from the following HIV vaccine trials were tested:HVTN 203 (246 vaccinees and 78 placebos; conducted by the HIV VaccineTrial Network), RV124 (conducted by the Walter Reed Army Institute ofResearch), VRC 004 (40 vaccinees and 10 placebos), VRC 006 (30 vaccineesand 6 placebos), VRC 009 (9 vaccinees and no placebos) and VRC 010 wereconducted by the Vaccine Research Center (NIAID, NIH), VAX 003 and VAX004 were conducted by VaxGen Inc. The HIV infection status of a givensample was provided by the collaborating groups and also determined byin house testing using the BioRad HIV-1/2 plus 0 kit (Bio Radlaboratories, Woodinwille, Wash.). Samples obtained from VRC 009 and VRC010 trials were also tested with the Capillus HIV-1/HIV-2 and Uni-GoldHIV rapid tests (Trinity Biotech, N.Y.).

Identification of HIV Sequences Recognized by Early Seroconversion SeraUsing Gene-Fragment Phage Display Library

In order to identify all the HIV sequences recognized by antibodiesgenerated soon after HIV infection, a gene-fragment phage displaylibrary (GFPDL) was constructed spanning the entire HIV-1 open readingframe of NL4-3. The HIV-1 GFPDL, contained more than 10⁷ independenttransformants. PCR-based analysis and sequencing of the insertsconfirmed that the library consisted of 100% recombinants, with aninsert size of 50-300 bp, and random distribution across the HIV genome.

Seven plasma samples constituting a seroconversion panel PRB-910(obtained from acutely HIV-1 infected individual; SeraCare BioServices,Gaithersburg, Md.) were used as bait for affinity selection of phagesdisplaying HIV-1 peptides. After four rounds of biopanning, 22 clones(for each plasma sample) were selected for insert sequencing, and wereanalyzed by phage ELISA with HIV positive and negative sera, to confirmthe specificity of reactivity. Alignment of inserts with the HIV-1genome led to identification of twelve immunodominant epitopes, mappingto Gag-p24 & p6, Pol, Env-gp120 & gp41, and Nef. Interestingly, phagesdisplaying sequences from the intracytoplasmic tail of gp41 (amino acids784-871) were repeatedly recognized by antibodies from both early (1-6months) and chronically infected individuals. The cytoplasmic tail ofgp41 was selected as the primary candidate for the differential assay asit is unlikely to be targeted by HIV-neutralizing antibodies, and it isnot included in most HIV vaccines currently under development. Inaddition, a p6 sequence was also selected, even though it was includedin early generation HIV vaccines, it contains very few HLA restrictedCTL epitopes (Frahm, N. et al. (2004) “CONSISTENT CYTOTOXIC-T-LYMPHOCYTETARGETING OF IMMUNODOMINANT REGIONS IN HUMAN IMMUNODEFICIENCY VIRUSACROSS MULTIPLE ETHNICITIES. J Virol 78:2187-2200) (Los Alamos database;http://hiv-web.lanl.gov). Importantly, the selected gp41 [spanning aminoacids 784-829 (SK1) and 836-871 (SK2)], and the p6 (amino acids 452-502)sequences are highly conserved among all HIV-1 M subtypes.

Establishment of the ‘HIV-SELECTEST’

The p6 and two gp41-derived peptides were chemically synthesized andused for the development of the new assay. Based on the Los Alamos HIVsequence database, consensus peptides were designed to encompass thegenetic variability among HIV-1 clades. Initially, each peptide wasevaluated individually to determine specificity and establish cut-offvalues. Since both gp41 peptides (SK1 and SK2) displayed similar verylow reactivity with HIV seronegative samples, the two were combined.Multiple ELISA conditions were tested and after screening of 1000seronegative samples, cut-off (CO) values for the gp41 (CO=0.03) and p6(CO=0.15) peptides were determined. Each CO value represents the averageabsorbance of negative sera+5 standard deviations. Additional panelscontaining high, intermediate, and low HIV-specific antibody titers wereused to determine the dynamic range of the assay. FIG. 7, Panels (a) and(b) demonstrate the binding of serially diluted representative plasma,PRB-204-06 (from SeraCare BioServices), in the p6 and gp41 ELISA,respectively. Multiple titrations with different samples demonstratedhigher maximum reactivity with the gp41 peptides and a broader dynamicrange when compared with the p6 peptide. Based on these analyses, allsubsequent ELISA testing was conducted with 1:100 dilution of sera orplasma. The HIV infection status of a given sample was determined bylicensed detection kits conducted either in-house or by an outsidelaboratory. An assay specificity of 100% for the gp41 peptides and 99.4%for the p6 peptide was established after screening of >2500 samples fromuninfected or from individuals infected with diverse HIV-1 clades. Thecombined sensitivity of the gp41 and p6 peptides is 99.3% for detectionof early and chronic infections in multiple geographical sites withclades A, B, C, D, E, F, J and multiple circulating recombinant forms.

Assay Robustness and Statistical Analysis

The reproducibility of the assay was determined by repeatedly testingnine HIV seropositive and three HIV seronegative samples from SeraCareBioServices. The distributions of the results obtained on multiple dateswere evaluated for normality and the appropriate p-values werecalculated using SigmaPlot. Representative plots are shown for oneindividual on the p6 and gp41 peptides (FIG. 7, Panels (c) and (d),respectively. The upper and lower limits (±2SD) represent the 95%confidence intervals. Inter-assay variability was ≦10% and intra-assayvariability was ≦5% for all the samples tested.

Acute Infections are Detected with HIV-SELECTEST

To determine how soon post-infection HIV-specific antibodies aredetected with the HIV-SELECTEST, several well-characterizedseroconversion panels were obtained from SeraCare BioServices containingsequential bleeds within 30-40 days of estimated exposure dates. Asshown in Table 12 top panel, the p6 peptide reacted positively withPBR-910 on collection day 26, in agreement with results obtained usinglicensed HIV antibody detection kits. The gp41 peptides were reactivewith the day 32 sample from the same individual. For PRB-929, day 25 andday 28 samples reacted with p6 and gp41 peptides, respectively (Table13). In that individual, infection was confirmed by PCR on day 14 andthe Abbott HIV Ag test was positive on day 18. In Tables 12 and 13,ELISA data for P6 and GP41 are shown as the ratio of test specimenabsorbance to cut-off value. Ratios of 1.00 or greater are consideredHIV seropositive and a sample ratio of less than 1 is considered HIVnegative; for Abbott assays, PCR, and FDA licensed EIA kits, HIV earlyseroconversion panels (within 6 weeks after HIV infection) and data forHIV RNA PCR quantification and FDA licensed serodiagnostic kits wereprovided by SeraCare BioServices, (Gaithersburg, Md.).

Similar results were obtained with additional seroconversion panels fromSeraCare BioServices, and demonstrated that HIV infection could bedetected by the HIV-SELECTEST within 2-4 weeks following HIV-1 RNAdetection by PCR, concurrent with the sensitivity limits of licensed HIVdiagnostic tests. In addition, we evaluated 28 seroconversion panelsspanning 6-18 months post-infection from Australia (Table 14). Withthese panels, p6 showed variable reactivity at later timespost-infection, whereas anti-gp41 reactivity increased over time and wasmaintained at high levels in most individuals, indicating that thekinetics and avidity of the antibody responses against the p6 and gp41epitopes were not linked. In Table 23, the date of infection wasestimated to be the midpoint between the last seronegative and firstseropositive results obtained with licensed HIV diagnostic kits.

Evaluation of Samples from HIV Vaccine Trials

The main proof-of-concept in support of the HIV-SELECTEST should comefrom evaluating the reactivity of vaccine induced antibodies in thecourse of prophylactic vaccine trials. To that end, six blinded panelsfrom completed vaccine trials (502 vaccinees) were tested including HVTN203 (conducted by the HIV Vaccine Trial Network), RV124 (conducted bythe Walter Reed Army Institute of Research) and VRC 004, VRC 006, VRC009, and VRC 010 (conducted by the Vaccine Research Center, NIAID, NIH).The description of the vaccine constructs used in the various trials andsummary of the results obtained with the HIV-SELECTEST appear in Table22. Canarypox vaccine constructs used in the RV124 and HVTN 203contained the p6 epitope used in the new assay. Additionally, theprotein boost in RV124 was gp 160. In contrast, the vaccine constructsused in VRC 004 and VRC 006 lacked the peptide sequences used in theHIV-SELECTEST.

TABLE 22 Summary of HIV-SELECTEST Reactivity with Vaccine Trial SamplesSponsor & Total No. of No. of HIV No. of Samples HIV-SELECTEST VaccineTrial Vaccine Composition Samples Infected Positive by FDA ReactivityNumber Prime Booster Tested Samples Licensed Kits (%) p6 (%) gp41 (%)RV124¹ vCP205 gp160 protein 79  0 63 (80%)  2 (2.5%) 0 (gag + pro + env)HVTN 203² vCP1452 (gag-pro- gp140 protein 324   2 97 (30%) 38 (12%) 2(0.6%)⁵ gp140 + Pol & Nef- CTL epitopes VRC 004³ pGag-Pol-Nef + SAME AS50⁶ 2 15 (38%)  1 (2%)⁵ 2 (4%)⁵   pEnvA + pEnvB + PRIME pEnvC VRC 006³Ad5-Gag-Pol + — 36⁶ 0 18 (60%) 0 0 Ad5-EnvA + Ad5- EnvB + Ad5-EnvC VRC009³ pGag-Pol-Nef + Ad5-Gag-Pol +  9⁶ 0  9 (100%) 0 0 pEnvA + pEnvB +Ad5-EnvA + pEnvC Ad5-EnvB + Ad5-EnvC VRC 010³ pGag + pPol +Ad5-Gag-Pol +  4⁶ 0  4 (100%) 0 0 pNef + pEnvA + Ad5-EnvA + pEnvB +pEnvC Ad5-EnvB + Ad5-EnvC ¹The RV124 vaccine immunogens contained boththe p6 & gp41 peptides used in the HIV-SELECTEST. ²The HVTN 203 vaccineimmunogen contained the p6 but not the gp41 sequences used inHIV-SELECTEST. ³The VRC 004, 006, 009 vaccines did not contain either p6or gp41 epitopes used in the HIV-SELECTEST, but participants in VRC 010received p6-containing DNA (pGag) prime during VRC 007 phase I trial.⁴Bio-Rad HIV-1/2 + O EIA kit was used for sample screening.Seroconversion in VRC 009 and VRC 010 was determined by rapid tests,Capillus HIV-1/HIV-2 and Uni-Gold HIV. ⁵Upon unblinding, theseseropositive samples were confirmed as true HIV infections. ⁶VRC 004 had10 placebo subjects and VRC 006 had 6 placebos, while VRC 009 and VRC010 had no placebo subjects.

The RV124 trial represents the worst case scenario, wherein all thepeptide sequences used in the HIV-SELECTEST were part of either thepriming or boosting immunogens. After the last boost (day 182), 80% ofvaccinees strongly seroconverted in commercial HIV-1 detection kits eventhough none were HIV infected (Table 22 and Table 20). However, only twoindividuals scored positive in the p6-ELISA, and none reacted in thegp41-ELISA. These findings suggested that the epitopes used in theHIV-SELECTEST were not very immunogenic in the context of the RV124vaccine constructs.

The HVTN 203 blinded specimens included samples from pre-vaccination andfour & six months post-vaccination obtained from 324 trial participants.In this panel, 30% of vaccinees seroconverted in the licensed HIVdetection assays, while only 12% reacted with the p6 peptide in theHIV-SELECTEST (Table 22). This finding was not surprising since theCanarypox/HIV prime (νCP1452) contained p6. Unexpectedly, two specimenswere repeatedly reactive with gp41 even though these sequences were notin the vaccine constructs. However, after unblinding, it was confirmedthat both samples were obtained from trial participants who got infectedduring this phase II trial.

The VRC phase I trials VRC 004, VRC 006, VRC 009, and VRC 010 wereconducted in 2002-2005. The DNA plasmids (VRC 004) and non-replicatingrecombinant Adenovirus serotype 5 vector (rAd5) (VRC 006) expressGag-Pol-Nef (in VRC 004) or Gag-Pol (in VRC 006) and multi-clade (A, B,C) envelope genes (gp145 in the DNA vaccine and gp140 in the rAd5vaccine). Among the 50 participants in VRC 004, 38% (15/40) ofvaccinated individuals seroconverted by licensed HIV diagnostic kits(Table 22). Unexpectedly, two samples reacted positive in the gp41ELISA, of which one sample also reacted with p6 in the HIV-SELECTEST(Table 22). Upon unblinding, it was determined that both individuals(both in the placebo arm) became infected during the VRC 004 trial. Inthe VRC 006 (Ad5/HIV), no intercurrent HIV infections were identified,yet 60% of vaccine recipients (18/30) tested positive in licensed HIVdetection tests. In contrast, none of the vaccinees reacted with eitherthe p6 or gp41 in the HIV-SELECTEST (Table 22). In VRC 009 and VRC 010,a subset of DNA vaccinated individuals (from VRC 004 and VRC 007 trials,respectively) was boosted with the rAd5/HIV vaccine. The 4 weekspost-boost samples demonstrated a very significant increase in totalHIV-specific antibodies (data not shown), and 100% seroconversion usingtwo licensed rapid tests (Capillus HIV-1/HIV-2 and Uni-Gold HIV, TrinityBiotech, N.Y.). Importantly, all vaccinees in these trials testednegative in the HIV-SELECTEST (Table 22).

Detection of Intercurrent HIV Infections During Vaccine Trials

Data obtained with the blinded panels from HIV vaccine trials tested todate indicates that vaccine-generated antibodies are most likely to givenegative reactivity in the HIV-SELECTEST, especially if the vaccines donot contain the p6 sequence. Importantly, the new test detected allintercurrent infections in the blinded samples. To further determine thesensitivity of new assay in detecting acute HIV infections in the courseof vaccine trials, sequential samples were tested from HIV infections incompleted Phase I, Phase II, and Phase III trials conducted by HVTN(Lee, D. et al. (2004) “BREAKTHROUGH INFECTIONS DURING PHASE 1 AND 2PRIME-BOOST HIV-1 VACCINE TRIALS WITH CANARYPDX VECTORS (ALVAC) ANDBOOSTER DOSE OF RECOMBINANT GP120 OR GP160,” J Infect Dis 190:903-907)VRC, and VaxGen (VAX 003/VAX 004 efficacy trials) (Gilbert, P. B. et al.(2005) “CORRELATION BETWEEN IMMUNOLOGIC RESPONSES TO A RECOMBINANTGLYCOPROTEIN 120 VACCINE AND INCIDENCE OF HIV-1 INFECTION IN A PHASE 3HIV-1 PREVENTIVE VACCINE TRIAL,” J Infect Dis 191:666-677 (2005).

As can be seen in Table 23, FIG. 6, Panel (a), and Table 24, sequentialsamples obtained from 22 vaccinees infected with HIV during the HVTNtrials and the VRC 004 trial reacted positive in the HIV-SELECTEST atearly time points after the estimated infection dates. Importantly, noreactivity in the HIV-SELECTEST was observed prior to HIV infections intrial participants, even though they were immunized with complex vaccineproducts.

TABLE 23 HIV-SELECTEST Specifically Detects Intercurrent HIV InfectionsDuring Multiple HIV Vaccine Trials Days After Estimated Date of HIV-Serum HIV SELECTEST Sample Infection¹ p6 gp41 Vaccine ImmunogenHIVNET-1-1 −102.00 0.52 0.13 vCP205 + SF-2 rgp120 HIVNET-1-2 71 0.7183.33 vCP205 + SF-2 rgp120 HIVNET-1-3 99 6.41 80.77 vCP205 + SF-2 rgp120HIVNET-2-1 −158.00 0.22 0.30 vCP205 + Saline placebo HIVNET-2-2 24 11.190.13 vCP205 + Saline placebo HIVNET-2-3 87 11.74 88.83 vCP205 + Salineplacebo HVTN 203-1-1 −22 0.32 0.13 vCP1452 mo (0, 1, 3, 6) + AIDSVAX B/Bmo (3, 6) HVTN 203-1-2 16 15.78 0.10 vCP1452 mo (0, 1, 3, 6) + AIDSVAXB/B mo (3, 6) HVTN 203-1-3 712 1.01 16.83 vCP1452 mo (0, 1, 3, 6) +AIDSVAX B/B mo (3, 6) AVEG-1-1 −9 0.67 0.10 vCP205 (mo 0, 1) + SF-2rpg120 (mo 6, 9, 12) AVEG-1-2 31 15.25 1.13 vCP205 (mo 0, 1) + SF-2rpg120 (mo 6, 9, 12) AVEG-1-3 72 16.51 46.33 vCP205 (mo 0, 1) + SF-2rpg120 (mo 6, 9, 12) VRC 004-1-1 −9 0.06 0.07 Placebo VRC 004-1-2 191.15 0.17 Placebo VRC 004-1-3 47 2.95 0.33 Placebo VRC 004-1-4 130 9.9723.07 Placebo ¹Sequential samples from HIV infections during VRC 004 andmultiple HVTN clinical trials and the estimated dates of infection wereprovided by the clinical oversight boards.

TABLE 24 Reactivity Of Intercurrent Hiv Infection Samples During HVTN &VRC-004 Clinical Trials In The ‘HIV-SELECTEST’ New HIV Serum Days PostELISA′ Sample Infection p6 gp41 Vaccine Type HVTN-1-1 −106.00 0.27 0.07vCP205 + rgp120 HVTN-1-2 71 1.92 8.10 HVTN-1-3 105.00 1.31 59.27HVTN-2-1 −19.00 0.08 0.13 Placebo-Saline HVTN-2-2 51 0.22 3.13 HVTN-2-367 0.17 33.00 HVTN-3-1 −67.00 0.04 0.13 Placebo-Saline HVTN-3-2 58 0.4046.70 HVTN-3-3 79 0.28 50.77 HVTN-4-1 −55.00 0.03 0.13 vCP205 + SalineHVTN-4-2 72 1.09 0.13 HVTN-4-3 85 1.15 0.17 HVTN-5-1 −102.00 0.52 0.13vCP205 + rgp120 HVTN-5-2 71 0.71 83.33 HVTN-5-3 99 6.41 80.77 HVTN-6-1−30.00 0.07 0.17 vCP205 + rgp120 HVTN-6-2 11 0.04 0.07 HVTN-6-3 53 0.7828.37 HVTN-7-1 −158.00 0.22 0.30 vCP205 + Saline HVTN-7-2 24 11.19 0.13HVTN-7-3 87 11.74 88.83 HVTN-8-1 −20.00 0.08 0.30 vCP205 + rgp120HVTN-8-2 30 0.35 0.23 HVTN-8-3 44 0.25 5.07 HVTN-9-1 −91.00 0.78 0.17vCP205 + Saline HVTN-9-2 106 4.22 14.33 HVTN-9-3 169.00 0.87 4.37HVTN-10-1 −52 0.49 0.10 vCP1452 HVTN-10-2 39 6.29 0.17 HVTN-10-3 52 5.162.33 HVTN-11-1 −14 0.09 0.10 vCP1452 + AIDSVAX B/B HVTN-11-2 91 0.6478.07 HVTN-12-1 −60 0.09 0.07 vCP1452 HVTN-12-2 38 0.45 6.03 HVTN-13-1−22 0.32 0.13 vCP1452 + AIDSVAX B/B HVTN-13-2 16 15.78 0.10 HVTN-13-3712 1.01 16.83 HVTN-14-1 −9 0.03 0.10 Placebo-Saline HVTN-14-2 5 0.050.20 HVTN-14-3 95 0.13 23.30 HVTN-15-1 −9 0.67 0.10 vCP205 + rgp120HVTN-15-2 31 15.25 1.13 HVTN-15-3 72 16.51 46.33 HVTN-16-1 −1030 0.390.13 vCP205 + gp160 HVTN-16-2 211 0.17 87.17 HVTN-16-3 307 0.13 92.33HVTN-17-1 −39.00 0.02 0.10 Placebo-Saline HVTN-17-2 37 0.11 23.67HVTN-17-3 66 0.15 44.70 HVTN-18-1 −408.00 0.05 0.10 vCP65 + rgp120HVTN-18-2 242.00 0.13 82.20 HVTN-18-3 272.00 0.16 85.63 HVTN-19-1 −90.000.37 0.13 vCP205 + rgp120 HVTN-19-2 92 3.97 31.10 HVTN-19-3 191.00 3.7077.33 HVTN-20-1 −37.00 0.03 0.07 Placebo-Saline HVTN-20-2 63 0.77 42.83VRC-004-1-1 −136 0.09 0.47 Placebo-Saline VRC-004-1-2 −40 0.28 0.37VRC-004-1-3 44 0.61 42.43 VRC-004-2-1 −13 0.05 0.07 Placebo-SalineVRC-004-2-2 14 1.15 0.17 VRC-004-2-3 69 2.95 0.33 VRC-004-2-4 145 9.9723.07

Sequential samples soon after the first confirmed PCR positive visitwere also obtained from 65 HIV infections during VAX 003 (AIDSVAX gp120B/E) and 81 HIV infections during VAX 004 (AIDS VAX gp120 B/B′) trialsconducted by VaxGen. The dates of PCR positively and seroconversion bylicensed HIV tests were provided by VaxGen. Table 25 contains analysisof two representative HIV infections in VAX 003 and VAX 004 trials thatdeveloped strong reactivity to p6 and gp41 peptides. Furthermore, theHIV-SELECTEST identified all intercurrent HIV infections within 90 daysof PCR confirmation (FIG. 6, Panels (b) and (c); Table 26 and Table 27,for VAX 003 and VAX 004, respectively).

TABLE 25 Early Diagnosis Of Intercurrent HIV Infections by HIV-SELECTESTDuring VaxGen Clinical Trials VAX 003 & VAX 004 HIV HIV HIV- Serum DrawPCR Seroconversion SELECTEST Sample Date Analysis¹ (EIA and WB) p6 gp41VAX-003-9-1 02/02/00 + − 0.69 0.23 VAX-003-9-2 16/02/00 + + 7.49 2.13VAX-003-9-3 09/03/00 + + 12.17 15.57 VAX-003-9-4 20/03/00 + + 14.42 70.4VAX-003-9-5 18/04/00 + + 7.18 45.53 VAX-003-14-1 01/02/01 + − 4.05 0.23VAX-003-14-2 15/02/01 + − 12.83 0.9 VAX-003-14-3 15/03/01 + + 8.21 12.33VAX-003-14-4 12/04/01 + + 7.32 12.3 VAX-003-14-5 10/05/01 + + 6.56 13.17VAX-004-9-1 17/02/99 + − 0.03 0.11 VAX-004-9-2 02/03/99 + − 0.31 0.15VAX-004-9-3 22/03/99 + − 4.73 1.04 VAX-004-9-4 06/04/99 + + 2.73 5.15VAX-004-51-1 14/12/98 + − 0.51 0.19 VAX-004-51-2 28/12/98 + − 3.15 0.3VAX-004-51-3 12/01/99 + − 5.69 14.22 VAX-004-51-4 27/01/99 + + 3.8751.33 ¹Sequential samples from HIV infections during VAX 003 and VAX 004clinical trials and the results of PCR and licensed HIV serodiagnosticassays were provided by the VaxGen clinical lab

TABLE 26 Reactivity of Intercurrent HIV Infections During VAX-003Clinical Trials in the HIV-SELECTEST HIV PCR A- HIV HIV- Serum Drawnaly- Seroconversion SELECTEST Sample Date sis¹ (EIA and WB) p6 gp41VAX-003-1-1 Jul. 15, 1999 + − 0.09 0.00 VAX-003-1-2 Jul. 29, 1999 + −0.06 0.17 VAX-003-1-3 Dec. 9, 1999 + + 1.47 59.60 VAX-003-1-4 Dec. 28,1999 + + 1.14 53.37 VAX-003-1-5 Jan. 4, 2000 + + 1.01 50.20 VAX-003-2-1Oct. 1, 2001 + − 0.07 2.20 VAX-003-2-2 Oct. 15, 2001 + + 0.13 21.20VAX-003-2-3 Nov. 7, 2001 + + 0.38 80.23 VAX-003-2-4 Dec. 4, 2001 + +0.23 87.30 VAX-003-3-1 Oct. 1, 2001 + − 0.58 0.20 VAX-003-3-2 Oct. 15,2001 + − 1.77 0.80 VAX-003-3-3 Mar. 26, 2002 + + 0.47 41.53 VAX-003-3-4Apr. 9, 2002 + + 4.31 81.17 VAX-003-3-5 May 17, 2002 + + 3.77 83.60VAX-003-4-1 Jan. 13, 2000 + − 0.04 0.27 VAX-003-4-2 Jan. 27, 2000 + −0.05 0.23 VAX-003-4-3 Jun. 26, 2000 + + 1.17 76.80 VAX-003-4-4 Jul. 14,2000 + + 0.79 63.17 VAX-003-4-5 Jul. 24, 2000 + + 0.59 69.27 VAX-003-5-1Apr. 24, 2002 + − 0.07 0.20 VAX-003-5-2 May 8, 2002 + + 0.08 0.73VAX-003-5-3 Aug. 28, 2002 + + 0.07 86.47 VAX-003-5-4 Dec. 11, 2002 + +0.08 82.63 VAX-003-6-1 Jun. 22, 1999 + − 0.10 0.23 VAX-003-6-2 Jul. 6,1999 + − 0.03 0.13 VAX-003-6-3 Jul. 22, 1999 + + 0.21 23.50 VAX-003-6-4Aug. 9, 1999 + + 0.11 89.90 VAX-003-6-5 Aug. 19, 1999 + + 0.18 93.50VAX-003-7-1 Jan. 9, 2001 + − 0.33 0.20 VAX-003-7-2 Jan. 23, 2001 + −1.28 0.73 VAX-003-7-3 Jun. 26, 2001 + + 0.25 39.43 VAX-003-7-4 Jul. 17,2001 + + 0.33 42.17 VAX-003-7-5 Jul. 27, 2001 + + 0.27 39.83 VAX-003-8-1Aug. 25, 1999 + − 0.19 0.10 VAX-003-8-2 Sep. 8, 1999 + − 12.41 0.43VAX-003-8-3 Jan. 20, 2000 + + 0.53 83.40 VAX-003-8-4 Jun. 13, 2000 + +0.19 83.97 VAX-003-8-5 Aug. 29, 2000 + + 0.32 89.20 VAX-003-9-1 Feb. 2,2000 + − 0.69 0.23 VAX-003-9-2 Feb. 16, 2000 + + 7.49 2.13 VAX-003-9-3Mar. 9, 2000 + + 12.17 15.57 VAX-003-9-4 Mar. 20, 2000 + + 14.42 70.40VAX-003-9-5 Apr. 18, 2000 + + 7.18 45.53 VAX-003-10-1 Jun. 6, 2000 + −0.07 0.23 VAX-003-10-2 Jun. 20, 2000 + − 0.11 0.13 VAX-003-10-3 Nov. 20,2000 + + 0.20 83.60 VAX-003-10-4 Dec. 18, 2000 + + 0.11 77.57VAX-003-10-5 Jan. 5, 2001 + + 0.11 84.07 VAX-003-11-1 Aug. 1, 2001 + −0.26 0.20 VAX-003-11-2 Aug. 15, 2001 + − 0.33 0.17 VAX-003-11-3 Jan. 16,2002 + + 0.48 2.87 VAX-003-11-4 Feb. 1, 2002 + + 1.90 14.10 VAX-003-11-5Feb. 15, 2002 + + 1.57 11.93 VAX-003-12-1 Mar. 15, 2000 + − 0.07 0.13VAX-003-12-2 Mar. 28, 2000 + − 0.22 0.10 VAX-003-12-3 Aug. 30, 2000 + +0.55 81.40 VAX-003-12-4 Sep. 11, 2000 + + 0.25 70.73 VAX-003-12-5 Sep.25, 2000 + + 0.41 80.20 VAX-003-13-1 Aug. 5, 1999 + − 0.06 0.17VAX-003-13-2 Aug. 19, 1999 + − 0.07 0.17 VAX-003-13-3 Sep. 2, 1999 + −0.08 0.03 VAX-003-13-4 Sep. 15, 1999 + − 0.33 1.80 VAX-003-13-5 Oct. 6,1999 + + 0.61 18.77 VAX-003-13-6 Nov. 16, 1999 + + 2.01 36.57VAX-003-13-7 Nov. 30, 1999 + + 0.91 35.37 VAX-003-14-1 Feb. 1, 2001 + −4.05 0.23 VAX-003-14-2 Feb. 15, 2001 + − 12.83 0.90 VAX-003-14-3 Mar.15, 2001 + + 8.21 12.33 VAX-003-14-4 Apr. 12, 2001 + + 7.32 12.30VAX-003-14-5 May 10, 2001 + + 6.56 13.17 VAX-003-15-1 Feb. 21, 2001 + −1.25 0.17 VAX-003-15-2 Mar. 8, 2001 + − 1.39 0.20 VAX-003-15-3 Aug. 29,2001 + + 0.79 88.90 VAX-003-15-4 Sep. 27, 2001 + + 0.71 81.17VAX-003-15-5 Oct. 24, 2001 + + 0.68 80.80 VAX-003-16-1 Oct. 20, 1999 + −0.23 0.13 VAX-003-16-2 Nov. 3, 1999 + − 0.37 0.27 VAX-003-16-3 Nov. 17,1999 + − 0.29 4.67 VAX-003-16-4 Dec. 1, 1999 + + 0.22 30.80 VAX-003-16-5Dec. 15, 1999 + + 0.16 66.13 VAX-003-16-6 Jan. 6, 2000 + + 0.22 82.23VAX-003-17-1 Sep. 22, 2000 + − 0.09 0.27 VAX-003-17-2 Oct. 6, 2000 + −0.09 0.30 VAX-003-17-3 Mar. 9, 2001 + + 0.36 83.40 VAX-003-17-4 Mar. 23,2001 + + 0.19 84.27 VAX-003-17-5 Apr. 9, 2001 + + 0.23 85.80VAX-003-18-1 Aug. 9, 1999 + − 0.20 0.17 VAX-003-18-2 Aug. 23, 1999 + −1.47 0.63 VAX-003-18-3 Sep. 6, 1999 + + 5.07 25.90 VAX-003-18-4 Sep. 17,1999 + + 2.89 39.00 VAX-003-18-5 Oct. 1, 1999 + + 2.39 69.73VAX-003-19-1 Aug. 14, 2001 + − 0.16 0.13 VAX-003-19-2 Sep. 3, 2001 + −0.11 0.47 VAX-003-19-3 Jan. 29, 2002 + + 0.27 14.53 VAX-003-19-4 Feb.20, 2002 + + 1.17 51.33 VAX-003-19-5 Mar. 6, 2002 + + 0.83 42.07VAX-003-20-1 Jan. 8, 2001 + − 1.37 25.63 VAX-003-20-2 Jan. 22, 2001 + +1.53 34.60 VAX-003-20-3 Feb. 5, 2001 + + 0.83 28.33 VAX-003-20-4 Feb.21, 2001 + + 0.79 40.83 VAX-003-21-1 Nov. 16, 1999 + − 0.21 0.20VAX-003-21-2 Nov. 30, 1999 + − 0.16 0.13 VAX-003-21-3 Dec. 14, 1999 + −0.19 0.17 VAX-003-21-4 Dec. 28, 1999 + + 0.24 1.13 VAX-003-21-5 Jan. 11,2000 + + 0.21 11.53 VAX-003-21-6 Jan. 28, 2000 + + 0.50 38.43VAX-003-22-1 Nov. 10, 1999 + − 1.91 0.03 VAX-003-22-2 Nov. 24, 1999 + −1.24 0.10 VAX-003-22-3 Apr. 21, 2000 + + 2.28 85.60 VAX-003-22-4 May 11,2000 + + 2.37 86.97 VAX-003-22-5 Nov. 2, 2000 + + 1.25 85.40VAX-003-23-1 Mar. 7, 2002 + − 0.31 0.10 VAX-003-23-2 Mar. 21, 2002 + −0.36 0.10 VAX-003-23-3 Aug. 21, 2002 + + 0.41 92.23 VAX-003-23-4 Sep.11, 2002 + + 1.97 93.60 VAX-003-23-5 Oct. 17, 2002 + + 2.98 94.47VAX-003-24-1 Jan. 19, 2000 + − 0.04 0.17 VAX-003-24-2 Feb. 2, 2000 + −0.05 0.07 VAX-003-24-3 Feb. 16, 2000 + + 0.15 0.47 VAX-003-24-4 Mar. 8,2000 + + 0.30 35.87 VAX-003-24-5 Mar. 15, 2000 + + 0.41 65.67VAX-003-25-1 Jan. 27, 2000 + − 0.12 0.17 VAX-003-25-2 Feb. 10, 2000 + −0.09 0.07 VAX-003-25-3 Feb. 23, 2000 + + 0.05 0.33 VAX-003-25-4 Mar. 13,2000 + + 0.13 13.23 VAX-003-25-5 Mar. 24, 2000 + + 0.12 17.23VAX-003-26-1 Feb. 1, 2000 + − 0.03 0.13 VAX-003-26-2 Feb. 17, 2000 + −0.37 0.10 VAX-003-26-3 Jun. 22, 2000 + + 1.33 80.00 VAX-003-26-4 Sep.13, 2000 + + 0.45 69.80 VAX-003-26-5 Nov. 6, 2000 + + 0.55 85.30VAX-003-27-1 Jan. 4, 2000 + − 1.99 0.27 VAX-003-27-2 Jan. 17, 2000 + −7.77 0.10 VAX-003-27-3 May 23, 2000 + + 6.41 71.83 VAX-003-27-4 Jun. 12,2000 + + 3.79 57.77 VAX-003-27-5 Jun. 19, 2000 + + 4.27 63.70VAX-003-28-1 May 11, 2000 + − 0.18 0.20 VAX-003-28-2 May 25, 2000 + −0.23 0.10 VAX-003-28-3 Oct. 25, 2000 + + 1.76 91.73 VAX-003-28-4 Nov.28, 2000 + + 0.95 90.67 VAX-003-28-5 Dec. 20, 2000 + + 1.42 94.77VAX-003-29-1 Jun. 13, 2000 + − 0.05 0.10 VAX-003-29-2 Aug. 3, 2000 + −0.30 87.20 VAX-003-29-3 Nov. 23, 2000 + + 0.20 92.07 VAX-003-29-4 Dec.22, 2000 + + 0.16 97.23 VAX-003-29-5 Jan. 8, 2001 + + 0.05 95.70VAX-003-30-1 Dec. 22, 1999 + − 0.04 0.10 VAX-003-30-2 Jan. 5, 2000 + −0.04 0.17 VAX-003-30-3 Jan. 18, 2000 + + 0.11 0.50 VAX-003-30-4 Jan. 31,2000 + + 0.13 16.50 VAX-003-30-5 Feb. 29, 2000 + + 0.09 36.33VAX-003-31-1 Dec. 29, 1999 + − 2.77 0.33 VAX-003-31-2 Jan. 12, 2000 + +3.89 0.50 VAX-003-31-3 Mar. 29, 2000 + + 7.35 8.90 VAX-003-31-4 May 12,2000 + + 4.45 12.83 VAX-003-32-1 Mar. 7, 2000 + − 1.83 0.10 VAX-003-32-2Mar. 21, 2000 + − 2.19 0.07 VAX-003-32-3 Jul. 25, 2000 + + 2.17 85.57VAX-003-32-4 Aug. 11, 2000 + + 0.72 81.80 VAX-003-32-5 Aug. 30, 2000 + +0.95 81.17 VAX-003-33-1 Jul. 25, 2000 + − 0.19 6.70 VAX-003-33-2 Aug. 8,2000 + + 0.23 12.43 VAX-003-33-3 Aug. 18, 2000 + + 0.09 5.17VAX-003-33-4 Sep. 8, 2000 + + 0.10 3.93 VAX-003-34-1 Oct. 16, 2001 + −0.05 0.17 VAX-003-34-2 Oct. 30, 2001 + − 0.04 0.17 VAX-003-34-3 Apr. 23,2002 + + 0.04 77.67 VAX-003-34-4 May 14, 2002 + + 0.15 91.90VAX-003-34-5 May 23, 2002 + + 0.18 91.90 VAX-003-35-1 Jan. 17, 2000 + −0.80 −0.03 VAX-003-35-2 Jan. 31, 2000 + − 3.61 0.70 VAX-003-35-3 Feb.14, 2000 + + 6.53 17.03 VAX-003-35-4 Mar. 3, 2000 + + 2.87 49.10VAX-003-35-5 Mar. 20, 2000 + + 2.45 77.63 VAX-003-36-1 Jan. 21, 2000 + −0.83 0.13 VAX-003-36-2 Feb. 7, 2000 + − 0.75 0.20 VAX-003-36-3 Feb. 16,2000 + − 0.56 0.47 VAX-003-36-4 Mar. 1, 2000 + − 0.78 12.83 VAX-003-36-5Apr. 5, 2000 + + 0.74 18.40 VAX-003-36-6 Apr. 24, 2000 + + 0.67 29.90VAX-003-36-7 May 12, 2000 + + 0.50 27.30 VAX-003-37-1 Jan. 24, 2001 + −0.08 0.10 VAX-003-37-2 Feb. 7, 2001 + − 0.63 1.13 VAX-003-37-3 Jul. 11,2001 + + 0.61 1.63 VAX-003-37-4 Aug. 3, 2001 + + 0.75 2.10 VAX-003-37-5Aug. 17, 2001 + + 0.67 4.47 VAX-003-38-1 Dec. 15, 2000 + − 0.06 0.13VAX-003-38-2 Dec. 28, 2000 + − 0.07 0.17 VAX-003-38-3 May 18, 2001 + +0.03 31.40 VAX-003-38-4 Jun. 1, 2001 + + 0.05 45.17 VAX-003-38-5 Jun.13, 2001 + + 0.05 54.13 VAX-003-39-1 Jan. 17, 2000 + − 0.49 0.27VAX-003-39-2 Jan. 31, 2000 + − 0.64 0.10 VAX-003-39-3 Feb. 14, 2000 + +0.89 0.17 VAX-003-39-4 Mar. 6, 2000 + + 0.55 9.70 VAX-003-39-5 Mar. 16,2000 + + 0.52 20.07 VAX-003-40-1 Jun. 19, 2001 + − 0.07 0.47VAX-003-40-2 Aug. 6, 2001 + + 0.09 9.77 VAX-003-40-3 Aug. 27, 2001 + +0.11 30.83 VAX-003-40-4 Sep. 14, 2001 + + 0.05 40.50 VAX-003-41-1 Nov.29, 2001 + − 0.07 0.13 VAX-003-41-2 Dec. 13, 2001 + − 0.09 0.13VAX-003-41-3 Mar. 11, 2002 + + 6.83 79.80 VAX-003-41-4 Mar. 26, 2002 + +9.95 90.63 VAX-003-41-5 Apr. 9, 2002 + + 8.75 92.20 VAX-003-42-1 Jan.19, 2000 + − 0.09 0.20 VAX-003-42-2 Feb. 2, 2000 + + 1.38 0.77VAX-003-42-3 Feb. 17, 2000 + + 0.69 13.77 VAX-003-42-4 Mar. 23, 2000 + +0.87 22.23 VAX-003-43-1 Jan. 15, 2002 + − 0.05 0.13 VAX-003-43-2 Jan.31, 2002 + − 0.06 0.20 VAX-003-43-3 Jul. 15, 2002 + + 0.09 63.87VAX-003-43-4 Aug. 7, 2002 + + 0.17 76.53 VAX-003-43-5 Aug. 21, 2002 + +0.15 81.37 VAX-003-44-1 Apr. 5, 2000 + − 0.05 0.17 VAX-003-44-2 Apr. 19,2000 + − 0.07 0.17 VAX-003-44-3 Sep. 7, 2000 + + 2.33 58.07 VAX-003-44-4Oct. 16, 2000 + + 1.18 39.40 VAX-003-44-5 Nov. 2, 2000 + + 0.73 34.37VAX-003-45-1 Mar. 7, 2002 + − 0.28 0.37 VAX-003-45-2 Mar. 20, 2002 + −0.22 0.23 VAX-003-45-3 Aug. 6, 2002 + + 0.21 78.80 VAX-003-45-4 Aug. 30,2002 + + 0.35 86.13 VAX-003-45-5 Sep. 10, 2002 + + 0.28 79.07VAX-003-46-1 Aug. 23, 2001 + − 2.05 49.57 VAX-003-46-2 Sep. 6, 2001 + −1.01 48.90 VAX-003-46-3 Feb. 7, 2002 + + 0.71 16.03 VAX-003-46-4 Mar.14, 2002 + + 1.06 76.90 VAX-003-46-5 May 30, 2002 + + 0.83 78.97VAX-003-47-1 May 9, 2000 + − 0.99 0.33 VAX-003-47-2 May 25, 2000 + −0.79 0.07 VAX-003-47-3 Jun. 8, 2000 + + 1.01 1.43 VAX-003-47-4 Aug. 2,2000 + + 0.29 63.67 VAX-003-47-5 Sep. 29, 2000 + + 0.26 72.13VAX-003-48-1 Apr. 26, 2000 + − 1.33 0.63 VAX-003-48-2 May 10, 2000 + +1.07 11.27 VAX-003-48-3 May 25, 2000 + + 0.40 52.40 VAX-003-48-4 Jun.23, 2000 + + 0.33 61.27 VAX-003-49-1 Apr. 24, 2001 + − 0.06 0.10VAX-003-49-2 May 9, 2001 + − 0.05 0.07 VAX-003-49-3 Sep. 20, 2001 + +0.95 89.80 VAX-003-49-4 Oct. 4, 2001 + + 0.99 86.63 VAX-003-49-5 Oct.26, 2001 + + 1.30 89.77 VAX-003-50-1 Apr. 1, 2002 + − 0.07 0.10VAX-003-50-2 Apr. 17, 2002 + − 0.08 0.23 VAX-003-50-3 Aug. 30, 2002 + +0.09 78.00 VAX-003-50-4 Sep. 20, 2002 + + 0.13 81.07 VAX-003-50-5 Nov.4, 2002 + + 0.14 82.93 VAX-003-51-1 Mar. 4, 2002 + − 2.40 0.13VAX-003-51-2 Mar. 21, 2002 + − 1.99 0.10 VAX-003-51-3 Aug. 20, 2002 + +0.27 71.43 VAX-003-52-1 Sep. 12, 2000 + − 0.27 1.07 VAX-003-52-2 Sep.26, 2000 + + 0.31 6.53 VAX-003-52-3 Oct. 11, 2000 + + 0.07 20.03VAX-003-52-4 Oct. 26, 2000 + + 0.13 10.07 VAX-003-53-1 Jun. 15, 2000 + −0.10 0.13 VAX-003-53-2 Jun. 28, 2000 + − 0.17 0.07 VAX-003-53-3 Nov. 1,2000 + + 0.41 10.53 VAX-003-53-4 Nov. 15, 2000 + + 0.23 7.20VAX-003-53-5 Nov. 28, 2000 + + 0.17 6.00 VAX-003-54-1 Jun. 12, 2000 + −1.93 0.07 VAX-003-54-2 Jun. 26, 2000 + − 3.84 0.10 VAX-003-54-3 Jul. 11,2000 + + 3.41 2.20 VAX-003-54-4 Jul. 26, 2000 + + 0.99 3.87 VAX-003-54-5Aug. 8, 2000 + + 2.02 20.30 VAX-003-55-1 Oct. 3, 2001 + − 0.09 0.17VAX-003-55-2 Oct. 17, 2001 + − 0.09 0.03 VAX-003-55-3 Mar. 18, 2002 + +0.37 27.47 VAX-003-55-4 Apr. 10, 2002 + + 0.84 64.53 VAX-003-55-5 Apr.24, 2002 + + 0.61 57.60 VAX-003-56-1 Jun. 12, 2000 + − 0.08 0.27VAX-003-56-2 Jul. 20, 2000 + − 0.24 10.27 VAX-003-56-3 Nov. 15, 2000 + +0.11 78.27 VAX-003-56-4 Dec. 19, 2000 + + 0.07 71.00 VAX-003-56-5 Jan.12, 2001 + + 0.05 76.80 VAX-003-57-1 Jun. 29, 2000 + − 0.05 0.30VAX-003-57-2 Jul. 13, 2000 + − 0.07 0.20 VAX-003-57-3 Nov. 16, 2000 + +0.69 53.63 VAX-003-57-4 Dec. 14, 2000 + + 0.32 22.80 VAX-003-57-5 Dec.21, 2000 + + 0.36 22.37 VAX-003-58-1 May 24, 2000 + − 0.13 0.17VAX-003-58-2 Jun. 7, 2000 + − 0.32 0.23 VAX-003-58-3 Jun. 23, 2000 + +0.43 9.57 VAX-003-58-4 Jul. 7, 2000 + + 1.70 37.17 VAX-003-58-5 Jul. 20,2000 + + 4.71 73.57 VAX-003-59-1 Apr. 17, 2002 + − 0.05 0.17VAX-003-59-2 May 1, 2002 + − 0.06 0.13 VAX-003-59-3 Oct. 1, 2002 + +0.26 49.53 VAX-003-59-4 Oct. 18, 2002 + + 0.85 81.63 VAX-003-60-1 Aug.30, 2002 + − 0.05 0.20 VAX-003-60-2 Sep. 13, 2002 + − 0.07 0.27VAX-003-60-3 Apr. 4, 2003 + + 0.68 50.27 VAX-003-61-1 May 15, 2001 + −0.07 0.27 VAX-003-61-2 May 30, 2001 + − 0.07 0.27 VAX-003-61-3 Oct. 31,2001 + + 0.12 57.97 VAX-003-61-4 Nov. 14, 2001 + + 0.21 82.40VAX-003-61-5 Nov. 29, 2001 + + 0.29 84.47 VAX-003-62-1 Nov. 21, 2002 + −0.05 0.17 VAX-003-62-2 Dec. 3, 2002 + − 0.07 0.20 VAX-003-62-3 May 7,2003 + + 0.37 89.37 VAX-003-63-1 Sep. 20, 2000 + − 0.33 0.13VAX-003-63-2 Oct. 4, 2000 + − 0.43 0.13 VAX-003-63-3 Feb. 13, 2001 + +3.66 86.27 VAX-003-63-4 Feb. 28, 2001 + + 2.82 83.40 VAX-003-63-5 Mar.13, 2001 + + 3.07 86.03 VAX-003-64-1 Jul. 5, 2000 + − 0.06 0.10VAX-003-64-2 Jul. 19, 2000 + − 0.10 0.17 VAX-003-64-3 Aug. 4, 2000 + +0.13 0.87 VAX-003-64-4 Aug. 25, 2000 + + 0.11 64.30 VAX-003-64-5 Sep. 6,2000 + + 0.06 66.97 VAX-003-65-1 Sep. 21, 2000 + − 0.16 0.10VAX-003-65-2 Oct. 5, 2000 + − 0.15 0.10 VAX-003-65-3 Feb. 21, 2001 + +0.49 26.87 VAX-003-65-4 Mar. 15, 2001 + + 1.53 38.03 VAX-003-65-5 Mar.28, 2001 + + 1.43 50.53

TABLE 27 Reactivity of Intercurrent HIV Infections During VAX-004Clinical Trials in the HIV-SELECTEST HIV PCR A- HIV HIV- Serum Drawnaly- Seroconversion SELECTEST Sample Date sis¹ (EIA and WB) p6 gp41VAX-004-1-1 Feb. 11, 2000 + − 0.03 0.15 VAX-004-1-2 Mar. 3, 2000 + −0.46 1.16 VAX-004-1-3 Apr. 3, 2000 + + 0.48 60.36 VAX-004-2-1 Feb. 14,2001 + − 0.50 0.37 VAX-004-2-2 Mar. 1, 2001 + + 0.82 1.84 VAX-004-3-1May 10, 2000 + − 0.07 0.11 VAX-004-3-2 May 25, 2000 + − 0.05 0.20VAX-004-3-3 Nov. 8, 2000 + + 0.25 103.48 VAX-004-4-1 Mar. 20, 2001 + −0.03 0.30 VAX-004-4-2 Apr. 2, 2001 + − 0.07 1.15 VAX-004-4-3 Oct. 3,2001 + + 0.05 99.60 VAX-004-5-1 Feb. 17, 1999 + − 0.07 0.19 VAX-004-5-2Mar. 3, 1999 + − 0.09 0.37 VAX-004-5-3 Mar. 17, 1999 + − 0.09 0.11VAX-004-5-4 Mar. 31, 1999 + − 0.13 0.30 VAX-004-5-5 Aug. 4, 1999 + +0.25 76.67 VAX-004-6-1 Sep. 21, 2000 + − 0.03 0.20 VAX-004-6-2 Oct. 3,2000 + − 0.33 0.15 VAX-004-6-3 Oct. 18, 2000 + + 0.92 3.48 VAX-004-7-1Jun. 14, 2000 + − 0.31 39.44 VAX-004-7-2 Dec. 18, 2000 + + 0.44 74.07VAX-004-8-1 May 1, 2001 + − 0.12 0.15 VAX-004-8-2 Aug. 8, 2001 + + 0.6399.37 VAX-004-9-1 Feb. 17, 1999 + − 0.03 0.11 VAX-004-9-2 Mar. 2, 1999 +− 0.31 0.15 VAX-004-9-3 Mar. 22, 1999 + − 4.73 1.04 VAX-004-9-4 Apr. 6,1999 + + 2.73 5.15 VAX-004-10-1 Oct. 13, 2000 + − 0.17 12.56VAX-004-10-2 Apr. 11, 2001 + + 0.07 16.56 VAX-004-11-1 Oct. 23, 1998 + −0.19 0.44 VAX-004-11-2 Nov. 3, 1998 + − 0.23 1.33 VAX-004-11-3 Nov. 18,1998 + + 0.18 4.37 VAX-004-12-1 Nov. 2, 2000 + − 0.09 1.37 VAX-004-13-1Feb. 11, 2000 + − 0.06 0.11 VAX-004-13-2 Aug. 10, 2000 + + 0.05 87.08VAX-004-14-1 Sep. 13, 2000 + − 1.97 1.63 VAX-004-14-2 Sep. 27, 2000 + +1.81 38.40 VAX-004-15-1 Jan. 25, 2001 + − 0.03 0.11 VAX-004-15-2 Feb. 8,2001 + − 0.12 0.22 VAX-004-15-3 Jul. 11, 2001 + + 0.02 8.72 VAX-004-16-1Feb. 22, 2001 + − 0.59 0.19 VAX-004-16-2 Mar. 8, 2001 + − 0.45 0.19VAX-004-16-3 Aug. 29, 2001 + + 1.00 82.28 VAX-004-17-1 Jul. 23, 1999 + −0.15 0.19 VAX-004-17-2 Aug. 6, 1999 + − 0.11 0.26 VAX-004-17-3 Aug. 20,1999 + + 0.27 2.19 VAX-004-18-1 Feb. 10, 2000 + − 0.06 0.26 VAX-004-18-2Jul. 27, 2000 + + 0.09 58.72 VAX-004-19-1 Dec. 5, 2000 + − 0.16 8.33VAX-004-19-2 Apr. 9, 2001 + + 0.65 59.85 VAX-004-20-1 Mar. 6, 2000 + −2.13 0.11 VAX-004-20-2 Mar. 22, 2000 + − 2.56 0.33 VAX-004-20-3 Oct. 3,2000 + + 1.43 106.70 VAX-004-21-1 Apr. 11, 2001 + − 0.01 0.04VAX-004-21-2 Jun. 14, 2001 + + 0.14 21.93 VAX-004-22-1 May 4, 2000 + −0.37 0.22 VAX-004-22-2 Sep. 12, 2000 + + 1.15 96.70 VAX-004-23-1 Oct.31, 2000 + − 0.20 0.96 VAX-004-23-2 Nov. 15, 2000 + + 0.20 13.12VAX-004-24-1 Oct. 6, 1999 + − 0.03 0.11 VAX-004-24-2 Oct. 21, 1999 + +3.92 0.60 VAX-004-25-1 Sep. 21, 2000 + − 0.14 0.22 VAX-004-25-2 Sep. 26,2000 + − 0.13 0.37 VAX-004-25-3 Oct. 16, 2000 + + 1.05 21.56VAX-004-26-1 Jan. 6, 1999 + − 0.02 0.15 VAX-004-26-2 Jan. 22, 1999 + −0.13 0.22 VAX-004-26-3 May 28, 1999 + + 0.63 18.44 VAX-004-27-1 Sep. 21,1999 + − 0.23 0.15 VAX-004-27-2 Oct. 14, 1999 + − 0.85 0.96 VAX-004-27-3Mar. 30, 2000 + + 1.39 35.00 VAX-004-28-1 Jan. 14, 2000 + − 0.07 0.11VAX-004-28-2 Jan. 28, 2000 + − 0.07 0.11 VAX-004-28-3 Jul. 11, 2000 + +0.31 87.04 VAX-004-29-1 Nov. 26, 2001 + − 0.19 0.20 VAX-004-29-2 Mar.18, 2002 + + 2.09 95.56 VAX-004-29-3 Apr. 8, 2002 + + 1.54 101.07VAX-004-30-1 Feb. 28, 2001 + − 0.05 0.26 VAX-004-30-2 Oct. 3, 2001 + +0.08 79.24 VAX-004-31-1 Oct. 20, 2000 + − 0.11 0.22 VAX-004-31-2 Nov. 6,2000 + − 0.11 2.33 VAX-004-31-3 Jun. 12, 2001 + + 0.21 111.12VAX-004-32-1 Oct. 11, 1999 + − 0.10 0.19 VAX-004-32-2 Oct. 25, 1999 + −0.11 0.11 VAX-004-32-3 Mar. 27, 2000 + + 0.81 52.40 VAX-004-33-1 Jun.15, 2000 + − 0.21 0.11 VAX-004-33-2 Sep. 29, 2000 + + 4.34 106.40VAX-004-34-1 Jan. 23, 2001 + − 0.40 3.04 VAX-004-34-2 Jan. 30, 2001 + +0.49 5.89 VAX-004-35-1 Oct. 27, 2000 + − 0.05 0.07 VAX-004-35-2 Nov. 3,2000 + − 0.12 0.15 VAX-004-35-3 Nov. 16, 2000 + − 0.13 0.52 VAX-004-35-4Dec. 7, 2000 + + 0.05 2.19 VAX-004-36-1 Jul. 24, 2000 + − 1.91 0.00VAX-004-36-2 Jul. 31, 2000 + + 4.55 0.24 VAX-004-37-1 Apr. 14, 1999 − −0.17 0.04 VAX-004-37-2 Jul. 14, 1999 + − 5.73 0.07 VAX-004-37-3 Jul. 21,1999 + + 8.76 0.74 VAX-004-38-1 Oct. 4, 2000 + − 0.03 0.11 VAX-004-38-2Oct. 19, 2000 + − 0.11 0.22 VAX-004-38-3 May 10, 2001 + + 1.52 88.93VAX-004-39-1 May 19, 1999 + − 0.04 0.15 VAX-004-39-2 Jun. 3, 1999 + −0.13 0.19 VAX-004-39-3 Jun. 17, 1999 + + 0.15 1.10 VAX-004-40-1 Jul. 30,1999 + − 0.06 0.11 VAX-004-40-2 Aug. 12, 1999 + − 0.07 0.22 VAX-004-40-3Dec. 30, 1999 + + 0.77 16.96 VAX-004-41-1 Jun. 11, 2001 + − 0.05 0.26VAX-004-41-2 Jun. 25, 2001 + + 1.24 0.28 VAX-004-42-1 Jun. 13, 2000 + −0.04 0.11 VAX-004-42-2 Jul. 20, 2000 + + 0.24 41.00 VAX-004-43-1 Aug.27, 1999 + − 0.21 0.22 VAX-004-43-2 Sep. 10, 1999 + − 0.50 0.26VAX-004-43-3 Mar. 10, 2000 + + 0.18 30.44 VAX-004-44-1 May 14, 2001 + −0.15 0.33 VAX-004-44-2 Aug. 24, 2001 + + 0.84 27.78 VAX-004-44-3 Sep. 7,2001 + + 0.61 24.04 VAX-004-45-1 Jul. 31, 2000 + − 0.04 0.22VAX-004-45-2 Aug. 10, 2000 + − 0.07 0.22 VAX-004-45-3 Feb. 19, 2001 + +0.07 10.16 VAX-004-46-1 Oct. 4, 1999 + − 1.63 0.11 VAX-004-46-2 Oct. 18,1999 + + 1.60 2.04 VAX-004-46-3 Oct. 27, 1999 + + 1.49 4.56 VAX-004-47-1Aug. 2, 2000 + − 0.97 0.19 VAX-004-47-2 Jan. 19, 2001 + − 5.58 18.04VAX-004-47-3 Feb. 8, 2001 + + 5.55 14.80 VAX-004-48-1 Sep. 7, 1999 + −0.15 0.15 VAX-004-48-2 Sep. 27, 1999 + − 0.14 0.48 VAX-004-48-3 Feb. 8,2000 + + 0.16 37.04 VAX-004-49-1 Nov. 14, 2000 + − 0.09 0.20VAX-004-49-2 Dec. 5, 2000 + + 3.11 0.78 VAX-004-50-1 Nov. 7, 2001 + −0.08 0.22 VAX-004-50-2 Nov. 21, 2001 + − 0.73 0.52 VAX-004-50-3 Dec. 18,2001 + + 1.67 88.28 VAX-004-51-1 Dec. 14, 1998 + − 0.51 0.19VAX-004-51-2 Dec. 28, 1998 + − 3.15 0.30 VAX-004-51-3 Jan. 12, 1999 + −5.69 14.22 VAX-004-51-4 Jan. 27, 1999 + + 3.87 51.33 VAX-004-52-1 Apr.2, 1999 + − 0.26 2.04 VAX-004-52-2 Apr. 16, 1999 + − 0.23 5.41VAX-004-52-3 Apr. 30, 1999 + + 0.55 15.15 VAX-004-53-1 Nov. 30, 2000 + −0.06 0.19 VAX-004-53-2 Dec. 14, 2000 + − 0.07 0.15 VAX-004-53-3 May 23,2001 + + 0.16 102.52 VAX-004-54-1 Mar. 30, 1999 + − 0.44 0.22VAX-004-54-2 Apr. 7, 1999 + − 1.36 0.48 VAX-004-54-3 Apr. 21, 1999 + +2.35 6.24 VAX-004-55-1 Sep. 14, 1999 + − 0.65 0.74 VAX-004-55-2 Oct. 4,1999 + + 2.07 4.44 VAX-004-56-1 Mar. 19, 2001 + − 0.05 0.19 VAX-004-56-2Aug. 15, 2001 + + 8.01 0.40 VAX-004-57-1 Jan. 24, 2002 + − 0.09 0.30VAX-004-57-2 Feb. 7, 2002 + + 0.19 3.44 VAX-004-57-3 Feb. 11, 2002 + +0.19 3.93 VAX-004-58-1 Feb. 9, 2000 + − 0.15 0.32 VAX-004-58-2 Aug. 8,2000 + + 0.19 38.12 VAX-004-59-1 Oct. 17, 2001 + − 0.04 0.15VAX-004-59-2 Nov. 9, 2001 + − 0.13 0.07 VAX-004-59-3 Mar. 14, 2002 + +0.24 84.33 VAX-004-60-1 Jul. 5, 2001 + − 0.07 0.30 VAX-004-60-2 Jul. 19,2001 + − 0.04 2.33 VAX-004-60-3 Nov. 9, 2001 + + 0.05 9.67 VAX-004-61-1Jun. 28, 1999 + − 0.47 0.59 VAX-004-61-2 Jul. 8, 1999 + + 0.35 1.20VAX-004-62-1 Feb. 23, 2000 + − 0.90 0.11 VAX-004-62-2 Mar. 7, 2000 + −0.55 0.19 VAX-004-62-3 Aug. 24, 2000 + + 0.81 1.08 VAX-004-63-1 Sep. 20,1999 + − 0.07 0.19 VAX-004-63-2 Oct. 7, 1999 + − 0.17 0.56 VAX-004-63-3Oct. 21, 1999 + + 0.26 3.84 VAX-004-64-1 Jun. 5, 2001 + − 0.03 0.11VAX-004-64-2 Oct. 23, 2001 + + 0.25 101.26 VAX-004-65-1 Oct. 8, 1999 + −0.05 0.22 VAX-004-65-2 Oct. 26, 1999 + − 0.03 0.11 VAX-004-65-3 Feb. 25,2000 + + 0.11 1.48 VAX-004-66-1 Sep. 3, 1999 + − 0.05 0.22 VAX-004-66-2Oct. 14, 1999 + − 0.04 1.22 VAX-004-66-3 Nov. 17, 1999 + + 0.16 9.00VAX-004-67-1 Jul. 8, 1999 + − 0.65 0.30 VAX-004-67-2 Jul. 20, 1999 + +0.51 1.03 VAX-004-67-3 Aug. 10, 1999 + + 1.10 21.59 VAX-004-68-1 Sep. 4,2001 + − 0.04 0.22 VAX-004-68-2 Jan. 29, 2002 + + 0.09 79.80VAX-004-69-1 Apr. 7, 1999 + − 0.20 0.11 VAX-004-69-2 Apr. 21, 1999 + −5.29 10.22 VAX-004-69-3 May 5, 1999 + + 4.98 48.76 VAX-004-70-1 Dec. 13,1999 + − 0.06 0.22 VAX-004-70-2 Jan. 4, 2000 + − 0.11 0.22 VAX-004-70-3Feb. 29, 2000 + + 0.15 14.92 VAX-004-71-1 Oct. 10, 2001 + − 0.41 0.19VAX-004-71-2 Oct. 25, 2001 + − 0.41 0.15 VAX-004-71-3 Mar. 20, 2002 + +1.13 94.68 VAX-004-72-1 Nov. 6, 2001 + − 0.05 0.30 VAX-004-72-2 Apr. 4,2002 + + 0.09 103.44 VAX-004-73-1 Feb. 23, 2001 + − 0.03 0.15VAX-004-73-2 Apr. 10, 2001 + + 0.49 20.00 VAX-004-74-1 Dec. 9, 1999 + −0.05 0.15 VAX-004-74-2 Jan. 11, 2000 + + 0.07 4.84 VAX-004-75-1 Aug. 2,2000 + − 0.04 0.59 VAX-004-75-2 Mar. 22, 2001 + + 0.05 26.48VAX-004-76-1 Feb. 26, 2002 + − 1.28 0.44 VAX-004-76-2 May 20, 2002 + +2.04 80.84 VAX-004-77-1 May 10, 2001 + − 0.07 0.07 VAX-004-77-2 Jul. 31,2001 + + 0.23 116.12 VAX-004-78-1 Oct. 14, 1999 + − 0.11 1.00VAX-004-78-2 Nov. 24, 1999 + + 1.43 2.12 VAX-004-79-1 Nov. 3, 1999 + −0.27 0.19 VAX-004-79-2 Nov. 17, 1999 + − 0.36 4.85 VAX-004-79-3 Mar. 23,2000 + + 0.16 1.08 VAX-004-80-1 Dec. 5, 2000 + − 0.07 0.26 VAX-004-80-2Apr. 23, 2001 + + 1.85 48.00 VAX-004-81-1 Feb. 24, 1999 + − 0.23 0.19VAX-004-81-2 Mar. 11, 1999 + − 0.25 0.22 VAX-004-81-3 Mar. 23, 1999 + −0.17 0.41 VAX-004-81-4 Apr. 6, 1999 + − 0.65 4.15 VAX-004-81-5 Aug. 25,1999 + + 0.24 94.26

It was also possible to compare the performance of the HIV-SELECTESTwith results obtained with the FDA-licensed kits provided by VaxGen(FIG. 7). In most cases, the earliest positive results were observedwith the same samples using the licensed diagnostics and theHIV-SELECTEST (dots falling on the diagonal lines). Surprisingly, 24intercurrent HIV infections in VAX 003, and 25 infections in VAX 004were detected earlier in the HIV-SELECTEST compared with the licensedkits [dots under the diagonal lines in FIG. 7, Panels (a) and (b)],displaying the efficacy of HIV-SELECTEST in early diagnosis of HIVinfection. Therefore, the new assay could be part of an algorithm thatwill provide an important differential diagnostic tool during futurephase III prophylactic vaccine trials and for testing of blood andtissue donors.

The use of a phage display library to clone and express the entire openreading frames of HIV afforded the opportunity to identify all theepitopes that are recognized by seroconversion antibodies during acuteHIV infection. Affinity selection of the phage display library usingseroconversion panels led to the discovery of new epitopes in gp41 andp6, which were selected to develop a new differential diagnostic test.

The results described above demonstrate that vaccine generatedantibodies scored either negative or weakly positive in theHIV-SELECTEST even when the p6 or gp41 sequences were part of thevaccine constructs (i.e., RV124 and HVTN 203). Furthermore, theHIV-SELECTEST detected all intercurrent HIV infections. It should benoted that while all intercurrent infections in the VAX 004 trial(conducted in the United States and the Netherlands) were with Glade Bviruses, all the HIV infections in the VAX 003 trial (conducted inThailand), were with Glade E variants, demonstrating the feasibility ofusing the HIV-SELECTEST outside the United States in a multicladescenario, which is a prerequisite for global vaccine trials. Together,these data provide strong proof of the specificity and sensitivity ofthe new p6 and gp41 peptide-based ELISA. They further suggest that iffuture vaccine candidates do not contain these epitopes all uninfectedvaccinees are expected to score negative in the new assay. In contrast,antibodies generated following intercurrent infections in the course ofHIV vaccine trials, or at later times, should be detected by theHIV-SELECTEST soon after infection.

This inexpensive and high-throughput assay could be added to thealgorithm of detection tests used in clinical sites and in blood andplasma collection centers. As such, this assay will be highly relevantfor early diagnosis of intercurrent HIV infections in future vaccinetrials, particularly in the setting of HIV vaccines that, while not ableto prevent infection, may reduce viral loads after acquisition.Importantly, the HIV-SELECTEST should help to alleviate the concernsregarding social and economic harms due to long-term seroconversion ofuninfected participants in preventive HIV vaccine trials.

Example 10 Improved Gag-p6 Peptide for HIV-1 Detection Assay

During the above-described testing, it was observed that some of thesera from individuals infected with Glade C viruses (mainly fromSouthern Africa) did not react strongly with the consensus Gag-p6employed (SEQ ID NO:3). The employed peptide was therefore altered toproduce a peptide denoted “Gag-p6-C-sub” that is better recognized byall plasma and serum samples from HIV-1 Glade C infected individuals.The sequence of the Gag-p6-C-sub peptide is provided below:

GAG-p6-C-sub (SEQ ID NO: 141)SRPEPTAPPA ESFRFEETTP APKQEPKDRE PLTSLKSLFG SDPLSQ1        10         20         30         40     46

While HIV detection assays may be conducted using the Gag-p6-C-sub (SEQID NO:141) peptide alone, or in conjunction with any other peptide(s),etc., it is particularly preferred to combine the Gag p6-C-sub peptide(SEQ ID NO:141) with peptides having the sequence of the consensusGag-p6 (SEQ ID NO:3) in the same ELISA plate.

All publications and patents mentioned in this specification are hereinincorporated by reference to the same extent as if each individualpublication or patent application was specifically and individuallyindicated to be incorporated by reference. While the invention has beendescribed in connection with specific embodiments thereof, it will beunderstood that it is capable of further modifications and thisapplication is intended to cover any variations, uses, or adaptations ofthe invention following, in general, the principles of the invention andincluding such departures from the present disclosure as come withinknown or customary practice within the art to which the inventionpertains and as may be applied to the essential features hereinbeforeset forth.

What is claimed is:
 1. A method for detecting the presence, or measuringthe concentration, of an anti-HIV-1 antibody in a biological sample of ahuman, wherein said method comprises conducting an immunoassaycomprising the steps of: (a) contacting said biological sample with apeptide having an epitope that is recognized by said anti-HIV-1antibody, said contacting being under conditions sufficient to permitsaid anti-HIV-1 antibody if present in said sample to bind to saidepitope and form a peptide-anti-HIV-1 antibody complex; (b) contactingsaid formed peptide-anti-HIV-1 antibody complex with an anti-HIV-1antibody binding molecule, said contacting being under conditionssufficient to permit said anti-HIV-1 antibody binding molecule to bindto anti-HIV-1 antibody of said formed peptide-anti-HIV-1 antibodycomplex and form an extended complex; and (c) determining the presenceor concentration of said anti-HIV-1 antibody in said biological sampleby determining the presence or concentration of said formed extendedcomplex; wherein said epitope is present on a peptide having an aminoacid sequence selected from the group consisting of SEQ ID NOs:1-11,49-56, 90 and
 141. 2. The method of claim 1, wherein said immunoassay isan ELISA.
 3. The method of claim 2, wherein said ELISA comprisesincubating said biological sample in the presence of a solid support,wherein said peptide is immobilized to said support, wherein saidsupport is coated with milk, and wherein said anti-HIV-1 antibodybinding molecule is selected from the group consisting of anti-humanIgG+IgM-Fc, anti-human IgG-Fc, anti-human-IgG+IgM, and anti-human IgG;said anti-HIV-1 antibody binding molecule being conjugated to an enzyme.4. The method of claim 1, wherein said immunoassay is animmunochromatographic assay.
 5. The immunoassay of claim 4, wherein insaid immunochromatographic immunoassay: in said step (a), saidbiological sample is placed in contact with a first porous carrier, saidfirst porous carrier containing said peptide, said peptide beingnon-immobilized and detectably labeled; in said step (b), said formedpeptide-anti-HIV-1 antibody complex is placed in contact with a secondporous carrier, said second porous carrier being in communication withsaid first porous carrier, and containing an immobilized anti-HIV-1antibody binding molecule; and in said step (c), the presence orconcentration of said anti-HIV antibody in said biological sample isdetermined by detecting the presence of said labeled peptide in saidsecond porous carrier.
 6. The method of claim 1, wherein said epitope ispresent on a peptide or protein having the amino acid sequence of SEQ IDNO:2, SEQ ID NO:3 or SEQ ID NO:141.
 7. The method of claim 6, whereinsaid epitope is present on a peptide or protein having the amino acidsequence of SEQ ID NO:2.
 8. The method of claim 6, wherein said epitopeis present on a peptide or protein having the amino acid sequence of SEQID NO:3 or SEQ ID NO:141.
 9. The method of claim 1, wherein said epitopeis present on a peptide or protein having the amino acid sequence of SEQID NO:50, SEQ ID NO:51, or SEQ ID No.
 55. 10. The method of claim 6,wherein said epitope is present on a peptide or protein having the aminoacid sequence of SEQ ID NO:50.
 11. The method of claim 6, wherein saidepitope is present on a peptide or protein having the amino acidsequence of SEQ ID NO:51.
 12. The method of claim 6, wherein saidepitope is present on a peptide or protein having the amino acidsequence of SEQ ID NO:55.
 13. A peptide or protein comprising an epitopethat is recognized by an anti-HIV-1 antibody, wherein said epitope ispresent on a peptide having the amino acid sequence of SEQ ID NO:3, SEQID NO:50, or SEQ ID NO:55.
 14. A peptide or protein having the aminoacid sequence of SEQ ID NO:3, SEQ ID NO:50, SEQ ID NO:55, or SEQ IDNO:141.
 15. An immunological complex comprising a peptide bound to ananti-HIV-1 antibody, wherein said anti-HIV-1 antibody is additionallybound to an anti-HIV antibody binding molecule, wherein said peptide orprotein comprises an epitope that is recognized by an anti-HIV-1antibody, said epitope being present on a peptide or protein having anamino acid sequence selected from the group consisting of SEQ IDNOs:1-11, 49-56, 90 and
 141. 16. A kit for detecting the presence, ormeasuring the concentration, of an anti-HIV-1 antibody in a biologicalsample of a human, wherein said kit comprises a hollow casing comprisinga multilayer filter system, and first and second porous carriers,wherein said second porous carrier is in communication with said firstporous carrier, and said first porous carrier is in communication withsaid multilayer filter system, a portion of which is accessible fromsaid casing; wherein: said first porous carrier contains anon-immobilized, labeled peptide or protein; and said second porouscarrier contains an immobilized, unlabeled antibody that binds to humanIgG; wherein said peptide or protein comprises an epitope that ispresent on a peptide having an amino acid sequence selected from thegroup consisting of SEQ ID NOs:1-11, 49-56, and
 90. 17. The kit of claim16, wherein said epitope is present on a peptide or protein having theamino acid sequence of SEQ ID NO:2, SEQ ID NO:3 or SEQ ID NO:141. 18.The kit of claim 16, wherein said epitope is present on a peptide orprotein having the amino acid sequence of SEQ ID NO:50, SEQ ID NO:51, orSEQ ID NO:55.
 19. The kit of claim 16, wherein said epitope is presenton a peptide or protein having the amino acid sequence of SEQ ID NO:90.20. A method for detecting the presence, or measuring the concentration,of an anti-HIV-2 antibody in a biological sample of a human, whereinsaid method comprises conducting an immunoassay comprising the steps of:(a) contacting said biological sample with a peptide having an epitopethat is recognized by said anti-HIV-2 antibody, said contacting beingunder conditions sufficient to permit said anti-HIV-2 antibody ifpresent in said sample to bind to said epitope and form apeptide-anti-HIV-2 antibody complex; (b) contacting said formedpeptide-anti-HIV-2 antibody complex with an anti-HIV-2 antibody bindingmolecule, said contacting being under conditions sufficient to permitsaid anti-HIV-2 antibody binding molecule to bind to anti-HIV-2 antibodyof said formed peptide-anti-HIV-2 antibody complex and form an extendedcomplex; and (c) determining the presence or concentration of saidanti-HIV-2 antibody in said biological sample by determining thepresence or concentration of said formed extended complex; wherein saidepitope is present on a peptide having an amino acid sequence selectedfrom the group consisting of SEQ ID NOs:101-102.
 21. A method fordetecting the presence, or measuring the concentration, of an anti-HIV-1antibody in a biological sample of a human, wherein said methodcomprises conducting an immunoassay comprising the steps of: (a)contacting said biological sample with an epitope set comprising atleast one epitope that is recognized by said anti-HIV-1 antibody,wherein said epitope set consists essentially of an HIV-1 GAG p6 epitopeor epitopes, an HIV-1 gp41 terminal region epitope or epitopes, or acombination of an HIV-1 GAG p6 epitope or epitopes and an HIV-1 gp41terminal region epitope or epitopes, said contacting being underconditions sufficient to permit said anti-HIV-1 antibody if present insaid sample to bind to epitopes in said epitope set and form anepitope-anti-HIV-1 antibody complex; (b) contacting said formedepitope-anti-HIV-1 antibody complex with an anti-HIV-1 antibody bindingmolecule, said contacting being under conditions sufficient to permitsaid anti-HIV-1 antibody binding molecule to bind to anti-HIV-1 antibodyof said formed epitope-anti-HIV-1 antibody complex and form an extendedcomplex; and (c) determining the presence or concentration of saidanti-HIV-1 antibody in said biological sample by determining thepresence or concentration of said formed extended complex.
 22. Themethod of claim 21, wherein said peptide set consists essentially of acombination of an HIV-1 GAG p6 epitope or epitopes and an HIV-1 gp41terminal region epitope or epitopes.
 23. A method for detecting thepresence, or measuring the concentration, of an anti-HIV-2 antibody in abiological sample of a human, wherein said method comprises conductingan immunoassay comprising the steps of (a) contacting said biologicalsample with an epitope set comprising at least one epitope that isrecognized by said anti-HIV-2 antibody, wherein said epitope setconsists essentially of an HIV-2 GAG p6 epitope or epitopes, an HIV-2Env-gp36 epitope or epitopes, or a combination of an HIV-2 GAG p6epitope or epitopes and an HIV-2 Env-gp36 epitope or epitopes, saidcontacting being under conditions sufficient to permit said anti-HIV-2antibody if present in said sample to bind to epitopes in said epitopeset and form an epitope-anti-HIV-2 antibody complex; (b) contacting saidformed epitope-anti-HIV-2 antibody complex with an anti-HIV-2 antibodybinding molecule, said contacting being under conditions sufficient topermit said anti-HIV-2 antibody binding molecule to bind to anti-HIV-1antibody of said formed epitope-anti-HIV-1 antibody complex and form anextended complex; and (c) determining the presence or concentration ofsaid anti-HIV-2 antibody in said biological sample by determining thepresence or concentration of said formed extended complex.
 24. Themethod of claim 23, wherein said peptide set consists essentially of acombination of an HIV-2 GAG-p6 epitope or epitopes and an HIV-2 Env-gp36epitope or epitopes.